La révolution industrielle, l’évolution technologique, la croissance démographique et l’urbanisation ont affecté non seulement l’économie ou la politique dans le monde mais également la santé environnementale. Divers types de polluants sont générés et introduits, de manière permanente, dans l’environnement via les effluents industriels, agricoles et/ou municipaux. Parmi ces polluants figurent les polluants organiques persistants ou POP qui sont susceptibles de développer une toxicité non négligeable pour la santé humaine et le bon fonctionnement de l’écosystème. En plus, ils sont détectés dans tous les composants de l’écosystème global, y compris l’atmosphère, les ressources en eaux, le sol, les sédiments et les biotes. Depuis la découverte des insecticides DDT dans les tissus humains, le sort et le comportement de ces polluants dangereux ont retenu l’attention de la recherche scientifique. Dans le présent travail, on s’intéresse essentiellement aux POP du type hydrocarbures aromatiques polycycliques (HAP) et ses dérivés méthylés (Me-HAP) ainsi que les polychlorobiphényles (PCB). La première partie de l’étude est consacré à l’évaluation de leur niveau de contamination dans différents compartiments de l’environnement. Leur occurrence et distribution ont été évaluées dans les phases dissoutes, particulaires et sédimentaires du système d’eaux douces du bassin versant de l'Escaut dans la zone transfrontalière France-Belgique dans le cadre du projet FRB-RégionNPC "BIOFOZI" suivi d’une étude écotoxicologique. La même investigation est réalisée sur des sols originaires du Nord-Pas-de Calais (France) et de Madagascar. La seconde partie contribue à une étude de faisabilité de traitement biologique de sols contaminés par les HAP. / The industrial revolution, technological change, population growth and urbanization have affected not only the economy and politics all around the world but also the environment. Various types of pollutants are generated and introduced permanently into the environment through industrial, agricultural and/or municipal discharges. These pollutants include the persistent organic pollutants or POPs which can develop dangerous effects to human health and the ecosystem. In addition, they are reported detected in all the environmental components including the atmosphere, water resources, soils, sediments and biota. Since the discovery of the insecticides DDT in human tissue, the fate and behavior of these type of hazardous pollutants have caught the interest of researchers. In this work, our target contaminants are polycyclic aromatic hydrocarbons (PAHs) and their methylated derivatives (Me-PAHs) and polychlorinated biphenyls (PCBs). The first part of our study investigated the contamination level of theses POPs in the different compartments of the environment (water, suspended solid matters, sediment, soil). Their occurrence and distribution were evaluated in the dissolved, particulate and sedimentary phases of the freshwater system of the Scheldt basin in the border area between France and Belgium in FRB-RegionNPC "BIOFOZI" program. An ecotoxicological risk assessment was also carried out. The same investigations were also conducted in soil samples originating from northern France and from Madagascar. The second part of the present work concern a feasibility study of PAHs-contaminated soil bio-treatment (bioremediation).

Bacterial contamination in water sources is a serious health risk and the sources of the bacterial strains must be identified to keep people safe. This project is the result of a collaboration effort at Cal Poly to develop a new library-dependent Microbial Source Tracking method for determining sources of fecal contamination in the environment. The library used in this study is called Cal Poly Library of Pyroprints (CPLOP). The process of building CPLOP requires students to collect fecal samples from a multitude of sources in the San Luis Obispo area. A novel method developed by the biologists at Cal Poly called pyroprinting is then applied on the two intergenic regions of the E. coli isolates from these samples to obtain their fingerprints. These fingerprints are stored in the CPLOP database. In our study, we consider any E. coli samples whose fingerprints match above a certain threshold to be in the same group of bacterial strain. However, there has not yet been a final MST method that produces an acceptable level of accuracy. In this thesis, we propose a two-step MST classifier that combines two previous works: pyro-DBSCAN and k-RAP. These algorithms were developed specifically for CPLOP. We call our classifier HAP - Hybrid Algorithm for Pyroprints. The classifier works as follows. Given an unknown isolate, the first step requires performing clustering on the known isolates in the library and comparing the unknown isolate against the resulting clusters. If the isolate falls into a cluster, its classification will be returned as the dominant species of that cluster. Otherwise, we apply the k-Nearest Clusters Algorithm on this isolate to determine its final classification. Ultimately, HAP provides us a set of 16 decision strategies that identify the host species of an unknown sample with high accuracy.

No description available.

<p>Nontypeable Haemophilus influenzae (NTHi) is a common commensal in the human nasopharynx that can cause localized respiratory tract diseases such as otitis media, bronchitis, and pneumonia. NTHi adheres to respiratory epithelial cells, a critical step in the process of colonization enabled by bacterial surface adhesive structures called adhesins. One group of NTHi adhesins are autotransporters, proteins that have an N-terminal signal sequence, a C-terminal &#946;-barrel domain, and an internal passenger domain with effector function. The goal of this work was to increase our understanding of two NTHi autotransporters, Hap and Hia.</p><p>Hap is a monomeric autotransporter that mediates adherence to epithelial cells and extracellular matrix (ECM) proteins. Hap also self-associates with protein on neighboring bacteria, resulting in bacterial aggregation and microcolony formation. The Hap passenger domain contains the regions responsible for adhesive activity. To define the molecular mechanism of Hap adhesive activity, we crystallized the Hap passenger domain. Characterization of the crystal structure revealed an N-terminal globular domain and a more ordered, prism-like C-terminal domain. Interestingly, Hap crystallized as a multimer, suggesting that Hap-Hap interactions occurred in the passenger domain. Progressive deletions of the &#946;-loops that comprise the C-terminal region disrupted Hap-Hap interactions and led to a defect in bacterial settling. To further support that the C-terminal domain was responsible for Hap-Hap interactions,</p><p>7</p><p>we purified the wild type and truncated passenger domains and conjugated the proteins to latex beads. By light microscopy we visualized bead aggregation when the wild type passenger domain was conjugated to the beads, but not when the truncated passenger domain was conjugated. These results show that the C-terminal portion of the Hap passenger domain is responsible for Hap-Hap interactions leading to multimerization. Hap multimerization could be important in microcolony formation that leads to biofilm formation in vivo.</p><p>The ECM binding domain in located in the final 511 amino acids of the Hap passenger domain. To pin-point the region of the ECM protein fibronectin that is recognized by Hap, we spotted small fragments of fibronectin onto nitrocellulose membranes and incubated the membrane with purified Hap passenger domain. Far Western analysis using Hap antibody revealed that the smallest fibronectin region necessary for binding was comprised of the first two type III repeats, FNIII(1-2). To define the regions of Hap responsible for interaction with fibronectin, we mutated motifs in the Hap passenger domain that are important for fibronectin binding in other bacterial proteins. Based on assessment by ELISA, many of the mutations located between amino acids 525-725 caused reduced bacterial binding to fibronectin. However, no mutation totally ablated binding, suggesting that a larger Hap region is involved in fibronectin binding.</p><p>8</p><p>In an additional study, we identified a relationship between Hap levels in the outer membrane and the expression of lipopolysaccharide (LPS) biosynthesis enzymes. Through Western and qPCR analysis, we found that mutation of the rfaF, pgmB, lgtC, kfiC, orfE, rfbP, lsgB and lsgD genes involved in the synthesis of LPS oligosaccharide core in H. influenzae strain Rd/HapS243A resulted in loss of Hap in the bacterial outer membrane and a decrease in hap transcript. In contrast, the same mutations had no effect on outer membrane localization of H. influenzae P5 and IgA1 protease or levels of the p5 or iga1 transcripts, suggesting a Hap-specific effect. Elimination of the HtrA periplasmic protease resulted in a return of Hap to the outer membrane and restoration of wild type levels of hap transcript. We speculate that the lack of certain LPS biosynthesis enzymes causes Hap to mislocalize and accumulate in the periplasm, where it is degraded by HtrA. This degradation then leads to a decrease in hap transcript. lgtC is one of several phase variable LPS biosynthesis genes. Using an antibody against the epitope formed in part by the lgtC gene product, we identified lgtC phase-off bacteria by Western analysis of colony blots. Consistent with our previous observations, in lgtC phase off bacteria Hap was absent from the outer membrane and hap transcript was reduced. By analyzing a lgtC/lic2A double mutant, we found that Hap localization in the outer membrane and hap transcript levels were not related to LPS size but instead to the functions of the LPS synthesis enzymes themselves. This relationship could be beneficial to bacteria in vivo as a way to regulate Hap expression.</p><p>9</p><p>Early models suggested that autotransporters do not require accessory factors for folding and OM insertion. However, mounting recent evidence has suggested that the Bam complex is required for OM localization of most &#946;-barrel proteins, including autotransporters. We studied the role of the Bam complex in OM localization of the trimeric autotransporter Hia. We expressed Hia in E. coli strains with mutations in the Bam complex and found that BamA and BamD were needed for Hia localization, while BamB, BamC, and BamE were not necessary. In further studies, we mutated the C-terminus of Hia and found that the final and third-to-last amino acids were the most important for outer membrane localization.</p><p>In summary, this work provides insights into the regulation and adhesive activity of Hap and the outer membrane localization of Hia. We have learned important details about these factors that shed light on aspects of H. influenzae disease and could lead to new antimicrobial therapies.</p> / Dissertation

Project (D. Miss.)--Trinity Evangelical Divinity School, 1989. / Includes bibliographical references (leaves 160-166).

No estudo da osteointegração, os resultados adquiridos através dos softwares analisadores de imagens contribuirão para que se tenha uma melhor visualização da interface tecido biológico/material implantado. O objetivo deste trabalho foi avaliar, por meio de estudos histológico, morfométrico e densitométrico, as interfaces tecido ósseo/materiais implantados em comparação com o grupo controle (coágulo), descrevendo qualitativa e quantitativamente os resultados dessas análises. Foram selecionados 16 coelhos, Oryctolagus cuniculus, com idade de 90 dias, sendo estes divididos em quatro grupos de quatro animais (G1, G2, G3 e G4), com períodos pós-operatórios de sete, 15, 21 e 35 dias. Em cada animal, foram feitos dois defeitos ósseos nas tíbias direitas, preenchidos com o biomaterial Composto Ósseo de Ricinus (C.O.R.) granulado e o Grupo Controle (coágulo); na tíbia esquerda, preencheu-se com o biomaterial Hidroxiapatita (HAP-91). Após a eutanásia, as peças cirúrgicas foram removidas, identificadas e submetidas às análises. A análise histológica evidenciou, para os dois biomateriais, um grande aporte de células osteoprogenitoras e, com o avanço dos períodos experimentais, a deposição de um tecido ósseo mais desenvolvido. Estes resultados qualitativos corroboraram com a análise morfométrica, evidenciando a osteointegração pela aproximação das corticais ósseas. Com o estudo densitométrico, pôde-se acompanhar, por imagens tridimensionais e coloridas, o desempenho de cada biomaterial implantado e o grupo controle com o tecido ósseo. Concluiu-se que os dois biomateriais implantados se comportam de uma maneira muito desejável para que se constituam como uma escolha de materiais substitutos da reposição óssea. / In the study of osseointegration, the results acquired through the images analysis softwares, contribute in order to have a better view of the biological tissue/ material implanted interface. The aim of this study was to evaluate through studies: histological, morphometric and densitometric, the interactions of bone tissue / implanted materials in comparison with the control group (clot), and describing qualitatively and quantitatively the results of these analyzes. Were selected 16 rabbits, Oryctolagus cuniculus, with 90 days of age and divided into four groups of four animals (G1, G2, G3 and G4), and postoperative periods of seven, 15, 21 and 35 days. In each animal, two bone defects were made on the right tibia, and were filled with the (C.O.R.) Compound Bone of granulated Ricinus biomaterial and control group (clot); and in the left tibia, filled it with (HAP-91) Hydroxyapatite biomaterial. After euthanasia, the tibial bone was removed, identified and submitted for analyzes. The histological analysis showed for both biomaterials, a large amount of osteoprogenitor cells and, with the advancement of the experimental periods, the deposition of more developed bone tissue. These qualitative results corroborated with the morphometric analysis, showing the osseointegration by approximation of the cortical bones. With the densitometric study, could be accompanied, by three-dimensional images and colorful, the performance of each implanted biomaterial and the control group with the bone tissue. It was concluded that both implanted biomaterials behave in a manner very desirable to be constituted as a choice of substitute materials for the bone replacement.

No estudo da osteointegração, os resultados adquiridos através dos softwares analisadores de imagens contribuirão para que se tenha uma melhor visualização da interface tecido biológico/material implantado. O objetivo deste trabalho foi avaliar, por meio de estudos histológico, morfométrico e densitométrico, as interfaces tecido ósseo/materiais implantados em comparação com o grupo controle (coágulo), descrevendo qualitativa e quantitativamente os resultados dessas análises. Foram selecionados 16 coelhos, Oryctolagus cuniculus, com idade de 90 dias, sendo estes divididos em quatro grupos de quatro animais (G1, G2, G3 e G4), com períodos pós-operatórios de sete, 15, 21 e 35 dias. Em cada animal, foram feitos dois defeitos ósseos nas tíbias direitas, preenchidos com o biomaterial Composto Ósseo de Ricinus (C.O.R.) granulado e o Grupo Controle (coágulo); na tíbia esquerda, preencheu-se com o biomaterial Hidroxiapatita (HAP-91). Após a eutanásia, as peças cirúrgicas foram removidas, identificadas e submetidas às análises. A análise histológica evidenciou, para os dois biomateriais, um grande aporte de células osteoprogenitoras e, com o avanço dos períodos experimentais, a deposição de um tecido ósseo mais desenvolvido. Estes resultados qualitativos corroboraram com a análise morfométrica, evidenciando a osteointegração pela aproximação das corticais ósseas. Com o estudo densitométrico, pôde-se acompanhar, por imagens tridimensionais e coloridas, o desempenho de cada biomaterial implantado e o grupo controle com o tecido ósseo. Concluiu-se que os dois biomateriais implantados se comportam de uma maneira muito desejável para que se constituam como uma escolha de materiais substitutos da reposição óssea. / In the study of osseointegration, the results acquired through the images analysis softwares, contribute in order to have a better view of the biological tissue/ material implanted interface. The aim of this study was to evaluate through studies: histological, morphometric and densitometric, the interactions of bone tissue / implanted materials in comparison with the control group (clot), and describing qualitatively and quantitatively the results of these analyzes. Were selected 16 rabbits, Oryctolagus cuniculus, with 90 days of age and divided into four groups of four animals (G1, G2, G3 and G4), and postoperative periods of seven, 15, 21 and 35 days. In each animal, two bone defects were made on the right tibia, and were filled with the (C.O.R.) Compound Bone of granulated Ricinus biomaterial and control group (clot); and in the left tibia, filled it with (HAP-91) Hydroxyapatite biomaterial. After euthanasia, the tibial bone was removed, identified and submitted for analyzes. The histological analysis showed for both biomaterials, a large amount of osteoprogenitor cells and, with the advancement of the experimental periods, the deposition of more developed bone tissue. These qualitative results corroborated with the morphometric analysis, showing the osseointegration by approximation of the cortical bones. With the densitometric study, could be accompanied, by three-dimensional images and colorful, the performance of each implanted biomaterial and the control group with the bone tissue. It was concluded that both implanted biomaterials behave in a manner very desirable to be constituted as a choice of substitute materials for the bone replacement.

Ett hållbart samhälle behöver ha en klimatvänlig snöröjning. Den traditionella snöröjningen är associerad med en del problem, exempelvis bidrar saltspridning till ökad korrosion av vägar och fordon, förorening av både ytvatten och grundvatten samt ökad mobilitet av tungmetaller. Ett hållbart alternativ är hydronisk markvärme, även kallat Hydronic Asphalt Pavement, HAP. Snösmältning med ett HAP-system sker genom att en varm fluid cirkulerar i rör under ytan som ska hållas snöfri. HAP- systemets energianvändning och snösmältningskapacitet är beroende av hur de värmande rören är placerade samt vilket styrsystem som används. Rapporten syftar till att öka förståelsen för hur styrsystemet och geometrin påverkar HAP-systemets energianvändning och snösmältningstid. En numerisk 2D-modell konstrueras i COMSOL Multiphysics vilken användes för att simulera styrsystemets och geometrins påverkan på HAP-systemet. Snön förenklades som en värmesänka till vilken modellen överförde värme via ett värmeflöde. En avgränsning i rapporten var att det bortsågs från vatten på ytan för att förenkla modellen. Resultatet bekräftar att HAP-systemets styrsystem och geometri har stor påverkan på dess energianvändning och snösmältningstid. Generellt ger en hög energianvändning kortare tid med snö på ytan. Det gör att om det är önskvärt att ha ett energisnålt system behöver en avvägning mellan energianvändning och tid med snö på ytan göras. Ett intermittent styrsystem bedöms vara ett bra alternativ då det ger relativt låg energianvändning och kort tid med snö på ytan. Om det inte finns en begränsning i energianvändning finns det flera styrsystem som kan ge en snöfri yta hela året. Ytans temperatur är den bästa styrparametern att använda för att minska både energianvändning och snösmältningstid. Då värmerören placeras grundare ökar energibehovet och tiden med snö på ytan minskar. Det är möjligt att placera värmerören djupare med bibehållen snöfri tid på ytan om styrsystemet anpassas efter djupet. En viktig anpassning är att styrsystemet ger en förvärmningseffekt, exempelvis att vägen börjar värmas då vägytans temperatur understiger 1°C. En ökning av avståndet mellan värmerören, CCrör, minskar energibehovet och tiden med snö på ytan ökar. Det bedöms vara möjligt att öka CCrör till 350 mm utan att generera för stora skillnader i temperaturprofilen över ytan då rördjupet är 100 mm eller 160 mm. Det styrsystem som gynnas mest av att öka CCrör till 350 mm är ”Grundfall”, vilken värmer vägen under hela vinterhalvåret. Energianvändningen minskar då med 132 kWh/m2 (22,9%) och den längsta ihållande tiden med snö på ytan ökar från 0 h till 4 h. Beroende på vad kraven på ytan är kan det vara möjligt att ha 350 mm som CCrör för de andra styrsystemen. HAP-systemet blir resurseffektivare och billigare vid konstruktion ju större CCrör som används, vilket är önskvärt. Resultatet visar att det är en liten minskning i energianvändning och snösmältningstid då isolering är under värmerören jämfört med ingen isolering. Detbedöms därför vara omotiverat ur både energisynpunkt och snösmältningsmässigt att använda isolering under värmerören på det sätt som undersökts i detta arbete. Det är en markant skillnad i energianvändning mellan ett styrsystem som är enklare och ett som är mer komplext. Om styrsystemet ”Intermittent” används i stället för ”Grundfall” vid Hamngatan i Karlstad skulle det generera en minskad energianvändning av 4,37 GWh fjärrvärme (58,5%), vilket motsvarar 199 ton CO2 per år. Resultatet understryker vikten att ett optimalt styrsystem används. Även en liten skillnad i energianvändning kan ge stora energimässiga besparingar eftersom det ofta är stora ytor som värms med ett HAP-system. För att kunna avgöra vilket styrsystem som är bäst lämpat behöver kraven på ytan bestämmas, vilket inte görs i arbetet, utan resultaten hålls generella. / A sustainable society need to have a climate friendly snow removal system. The traditional snow removal systems generate some problems, for example increased corrosion of roads and vehicles, contamination of both surface- and ground water and increased mobility of heavy metals. A sustainable alternative is Hydronic Asphalt Pavement, HAP. Snow melting with a HAP-system is generated by circulating a warm fluid in pipes underneath the surface that is to be snow free. Both the energy usage and snow melting time is affected by how the heat pipes are placed and which control system that is used. The report aims to increase the knowledge of how both the control system and geometry of the heating pipes affect the energy use and snow melting time of a HAP-system. A numerical 2D-model was constructed in COMSOL Multiphysics which was used to simulate how the control system and geometry of the heating pipes effects the HAP-system. The snow was simplified to a heat sink, to which the model could transfer heat through a convective heat flux. A demarcation of the study is that water on the surface is ignored to simplify the model. The results confirms that both the control system and geometry of the heat pipes greatly affects the energy usage and snow melting time. In general, a large energy usage generates a shorter total time with snow on the surface. It is therefore needed to do a balancing between energy usage and the total time with snow on the surface if the energy usage is to be restricted. An intermittent control system is considered to be a good alternative as it gives a relative low energy usage and short time with snow on the surface. If there is no limitation on the energy use, there is several control systems that gives a snow free surface throughout the year. The surface temperature is the best parameter for the control system as it minimizes both the energy usage and snow melting time. When the heating pipes is placed shallower the energy usage is increased and the time with snow on the surface decreases. It is possible to place the heating pipes at a greater depth and still have the same functionality of the HAP-system if the control system is adjusted accordingly. One important adjustment for the control system is preheating, for example that the heating is turned on when the air temperature is less than 1°C. An increase of CCrör decrease the energy usage and increase the time with snow on the surface. It is possible to increase CCrör to 350 mm and still have a smooth temperature profile if the heating pipes is placed 100 mm or 160 mm beneath the road surface. The control system that gains the most out of an increase in !!!ö! to 350 mm is “Grundfall”, which reduce its energy usage with 132 kWh/m2 (22,9%) and the longest time with snow on the surface is increased from 0 h to 4 h. Depending on which demands the surface is to meet, it is possible to have 350 mm as CCrör for the other control systems. An increase in CCrör makes the HAP-system more resource efficient and cheaper to build, which is desirable. The results show a small decrease in energy usage and snow melting time when isolation is underneath the heating pipes compared to without isolation. It is therefore deemed to be unmotivated to use isolation as it is used in this paper, in both energy use- and snow melting time-perspective. There is a significant difference in energy use between a simple and more complex control system. If the control system “Intermittent” is used instead of “Grundfall” at Hamngatan in Karlstad the energy usage would decrease with 4,37 GWh heat (58,5%) and 199 ton of CO2. The result underlines the importance of an optimal control system for a HAP-system. Even a small change in energy consumption can generate large energy savings due to the scale of the surfaces that is heated with HAP-systems. To be able to decide which control system that is the best suited, the demand on the surface needs to be set. The demands are not set in this paper in order to keep the results general.

Ce travail a eu pour objectif d’étudier l’oxydation hétérogène de composés aromatiques polycycliques (CAP) adsorbés sur des particules solides, exposés à des oxydants troposphériques. Après adaptation et validation des protocoles analytiques, deux aspects ont été abordés : les cinétiques de dégradation avec O3, NO2 et OH dans un premier temps, puis l’étude des produits d’oxydation formés au cours de ces réactions. Les constantes de vitesse mesurées ont permis de comparer les différences de réactivité entre les composés étudiés (pyrène, 1-nitropyrène, 1-hydroxypyrène, 9,10-anthraquinone). L’influence de différents paramètres sur la réactivité (nature des particules, concentration en HAP…) a aussi été étudiée. Enfin, la détermination des produits d’oxydation et leur quantification, quand cela a été possible, a permis de mieux comprendre le devenir de ces composés particulaires dans l’atmosphère, à travers les mécanismes réactionnels proposés. / This work deals with the study of the atmospheric heterogeneous oxidation of polycyclic aromatic compounds (PACs) adsorbed on particles. After the development and the validation of the different analytical procedures, degradation kinetics and oxidation products were investigated for the reactions of NO2, OH and O3 with pyrene, 1-nitropyrene, 1-hydroxypyrene and 9,10-anthraquinone. The measured rate constants allowed to compare the reactivity of the different compounds. The influence of some parameters on the reactivity (nature of particles, PAC concentration…) has also been studied. Finally, the corresponding oxidation products were also measured, and quantified when possible, allowing to a better understanding of the fate of particulate PACs in the atmosphere, through the proposed chemical mechanisms.

Ce travail a eu pour objectif d'étudier l'oxydation hétérogène de composés aromatiques polycycliques (CAP) adsorbés sur des particules solides, exposés à des oxydants troposphériques. Après adaptation et validation des protocoles analytiques, deux aspects ont été abordés : les cinétiques de dégradation avec O3, NO2 et OH dans un premier temps, puis l'étude des produits d'oxydation formés au cours de ces réactions. Les constantes de vitesse mesurées ont permis de comparer les différences de réactivité entre les composés étudiés (pyrène, 1-nitropyrène, 1-hydroxypyrène, 9,10-anthraquinone). L'influence de différents paramètres sur la réactivité (nature des particules, concentration en HAP...) a aussi été étudiée. Enfin, la détermination des produits d'oxydation et leur quantification, quand cela a été possible, a permis de mieux comprendre le devenir de ces composés particulaires dans l'atmosphère, à travers les mécanismes réactionnels proposés.