La maladie de Crohn (MC) est caractérisée par une inflammation intestinale chronique affectant potentiellement n'importe quel segment du tube digestif. L’étiologie de la maladie reste encore inconnue, cependant, la théorie la plus largement acceptée repose sur une réponse inflammatoire anormale dirigée contre le microbiote intestinal chez un hôte génétiquement prédisposé. Plusieurs études ont démontré que la muqueuse iléale de patients atteints de MC est anormalement colonisée par des souches de Escherichia coli adhérentes et invasives (AIEC). Toutefois, à ce jour, au Brésil, aucune étude ne démontre la présence de telles souches d’E. coli chez les patients atteints de MC. Le but de cette étude était d'isoler et de caractériser les souches de E. coli chez les patients atteints de MC au Brésil. Les biopsies ont été réalisées sur 35 sujets, 24 atteints de MC et 11 contrôles. La colonisation par des entérobactéries associées à la muqueuse iléale de patients atteints de MC a été montré élevée par rapport au groupe contrôle. Parmi les 270 souches isolées, 241 ont été identifiées comme étant des E. coli : 183 à partir de patients atteints de MC et 58 des contrôles. La recherche de différents groupes phylogénétiques de E. coli a été réalisée par PCR. Il n'y a pas de différence significative entre la répartition des groupes phylogénétiques des souches de E. coli isolées dans le groupe témoin et les patients MC. Les capacités d'adhésion et d’invasion des souches aux cellules épithéliales intestinales humaines I-407 ont été analysées, aussi bien que sa capacité à survivre et se multiplier en macrophages humains THP-1. L'analyse moléculaire par PCR a également été réalisée pour la détection des facteurs de virulence et la présence de polymorphismes génétiques associées à des souches AIEC. Dans cette étude, seuls quelques- uns des isolats de E. coli présentaient des propriétés invasives et la capacité de survivre dans les macrophages. En outre, l’analyse de la séquence fimH des souches de E. coli isolées dans cette étude n'a pas révélé la sélection de polymorphismes dans l’adhésine FimH, comme décrit pour la collection de souches AIEC isolées chez des patients européens. Ces résultats ont donc permis de montrer que les souches isolées chez les patients atteints de MC brésiliens n’ont probablement pas encore co-évolué avec leur hôte pour développer un phénotype adhérent-invasif fort, mais il sera essentiel de suivre à l'avenir l'évolution des ces souches dans la population brésilienne pour comprendre la sélection et l'évolution du phénotype AIEC. / Crohn's disease (CD) is characterized by chronic intestinal inflammation potentially affecting any segment of the digestive tract. The etiology of the disease is still unknown, however, the most widely accepted theory relies on an abnormal inflammatory response directed against the gut microbiota in a genetically predisposed host. Several studies have shown that the ileal mucosa of patients with CD is abnormally colonized by adherent and invasive Escherichia coli strains (AIEC). However, to date, in Brazil, no study has demonstrated the presence of such E. coli strains. coli in patients with CD. The purpose of this study was to isolate and characterize E. coli strains in patients with CD in Brazil. Biopsies were performed on 35 subjects, 24 with MC and 11 controls. Colonization with enterobacteria associated with the ileal mucosa of MC patients was shown to be elevated relative to the control group. Of the 270 strains isolated, 241 were identified as E. coli: 183 from CD patients and 58 controls. The search for different phylogenetic groups of E. coli was performed by PCR. There is no significant difference between the distribution of phylogenetic groups of E. coli strains isolated in the control and MC patients. The adhesion and invasion abilities of strains to human intestinal epithelial cells I-407 were analyzed, as well as its ability to survive and multiply into human macrophages THP-1. PCR molecular analysis was also performed for the detection of virulence factors and the presence of genetic polymorphisms associated with AIEC strains. In this study, only a few of the E. coli isolates had invasive properties and the ability to survive in macrophages. In addition, analysis of the fimH sequence of E. coli strains isolated in this study did not reveal the selection of polymorphisms in the FimH adhesin, as described for the collection of AIEC strains isolated from European patients. These results have thus shown that strains isolated from patients with Brazilian CD probably have not yet co-evolved with their host to develop a strong adherent-invasive phenotype, but it will be essential to monitor the future evolution of these strains in the Brazilian population to understand the selection and evolution of the AIEC phenotype.

Competition between native perennial grasses and Bromus tectorum has been studied for many years. Recently, soil nutrients have been immobilized in an effort to preferentially inhibit growth of B. tectorum relative to native species. Most of this work has focused on soil N, but interactions with soil P are less studied and may be important as well. Additionally, although competitive effects and nutrient responses of several Centaurea spp. are well documented, data are lacking on the competitive effects that Centaurea virgata exerts on the establishment of native and exotic communities. A field experiment and a greenhouse experiment were conducted to evaluate influence of N and P on the native perennial bunchgrass Pseudoroegneria spicata in competition with B. tectorum and C. virgata. Chapter 2 describes the effects of nutrient immobilization and subsequent 2 x 2 factorial additions of N and P. Treatments were applied to transplanted individuals of the study species in monocultures and mixtures. Analysis of variance (ANOVA) was performed on shoot dry mass, soil water content, and physiological responses including photosynthetic rate, stomatal conductance, and transpiration. Results suggest that B. tectorum may be P-limited in certain circumstances, and that physiological activity of all species is subject to interactions between available N and P. In Chapter 3, I assess response of the study species to 2 x 2 factorial additions of N and P on a very low-nutrient soil in a greenhouse. Relative effects of different species mixtures on P. spicata are reported. I report ANOVA results of tiller number, leaf number, specific leaf area, shoot dry mass, root dry mass, and water addition. Results indicate that N and P co-limit P. spicata and B. tectorum, and to a lesser extent, C. virgata. B. tectorum showed the highest percentage response to fertilization. Land managers may be more successful establishing native grasses if they can minimize soil fertility.

Abandoned agricultural lands in the Intermountain West are plagued by dense, persistent non-native vegetation. Targeted restoration tools are required to remove the competitive advantage of these non-natives while also removing the soil legacies they leave behind. Activated carbon (AC) is one such tool, with the ability to disrupt the mechanisms of allelopathy, positive plant-soil feedbacks, and altered nutrient cycling commonly used by non-native species. Previous studies have shown the success of high concentrations of AC in native plant community restoration on a small scale. Here, our goals are twofold: first, to test AC effectiveness in restoring desirable plant communities on a larger scale, and secondly, to identify the primary mechanism, allelopathy versus microbial changes, through which AC impacts native and non-native species. A large scale AC treatment in Methow Valley, Washington tested the effectiveness of AC restoration at a large scale and tested five concentrations and two types of AC to determine lowest effective application. Following treatment, sites were monitored for vegetation cover for three years. The large-scale application produced similar results to the previous study at a 1000 g/m2 application rate, with a 28% increase in the ratio of desirable:undesirable species cover and a decrease to 25% undesirable species cover. However, the effectiveness of AC concentrations below 1000 g/m2 cannot yet be determined and may require a longer time scale and additional monitoring to assess restoration success. A greenhouse experiment was performed, which used native and non-native species common to the study site, grown in pairs in sterilized and live AC-treated soils to separate AC effects on allelopathy from that of microbial interactions. Both native and non-native species experienced a 25% decreased biomass in AC-treated live soils, with a minimal decrease in A- treated sterile soils for native species and no effect in AC-treated sterile soils for non-native species. Overall, AC live soils produced a positive effect on relative abundance; the ratio of native to non-native biomass was highest in AC-treated live soils. From these results, it is concluded that the primary pathway through which AC works is changes in the plant-microbial interactions of both native and non-native species.

Non-native invasive plant species can often have negative effects on native ecosystems, such as altered nutrient cycling, decreased habitat for wildlife, and outcompeting native plants. Around the Great Salt Lake (GSL), Utah, the invasive wetland grass Phragmites australis has become abundant in wetlands around the lake. Phragmites is replacing many native wetland plants provide important waterfowl habitat around the GSL. For successful management of Phragmites in GSL wetlands, it is important to know the current distribution of Phragmites, as well as areas that might be vulnerable to future invasion by Phragmites. To do this, we used multispectral aerial imagery to map the current distribution of Phragmites. We then created a model that statistically related the Phragmites distribution data to a suite of environmental predictor variables such as salinity, proximity to nutrient sources, or proximity to roads. Results from our model suggest that Phragmites is more likely to be found in wetland areas close to point sources of pollution, with lower elevations with prolonged inundation, and with moderate salinities. We used these results to identify areas around GSL that might be vulnerable to future invasion. Results from our study will assist wetlands managers in prioritizing areas for Phragmites monitoring and control by closely monitoring areas of prime Phragmites habitat.

Understanding of bio-nano-interfaces of living mammalian cells will benefit the identification of cellular alterations (e.g. nucleic acids, amino acids, biomechanics, etc.) due to external stimuli, the design of biomaterials (e.g. nanoparticles, nanotubes) and the investigation of the interaction between cells and bio-nano-interfaces (e.g. cell differentiation on 3D nanostructured materials). Analytical techniques can be applied to evaluate the chemical, physical, and mechanical properties of mammalian cells when exposed to such bio-nano-interfaces. In this study, non-invasive advanced spectroscopy techniques including atomic force microscopy (AFM) and Raman microscopy (RM), in conjunction with traditional biological methods are utilized to elucidate specific characteristic information for biological samples and how these property changes reflect the interaction with external stimuli. The focus of this dissertation is on the biophysical, biochemical and cytotoxic detection of mammalian cells interacting with bio-nano-interfaces, and this dissertation can be classified into three topics: biomechanics/cellular biopolymers measurement, bio-interfaces and nano-interfaces studies. For the topic of biomechanics/cellular biopolymers measurement, cellular biophysical and biomechanical properties could be used as differentiation markers to classify cellular differentiation. For the bio-interfaces part, it was observed that BRMS1 expression changed cellular biochemical and biomechanical properties, and the expressions of reactive oxidative species (ROS), apoptosis and cell viability of five types of cells displayed similar patterns over doxorubicin (DOX) incubation time. Secondly, A549 cells were treated with diesel exhaust particles (DEP) and resveratrol (RES) to study the effect of RES on the DEP-induced cells, and it was found that RES can alleviate DEP intervention on cellular structure and increase DEP-induced biomechanical and inflammatory changes. For the nano-interfaces topic, first we synthesized a hybrid nanoparticle with the multimodal properties of fluorescence imaging, Surface-enhanced Raman spectroscopy (SERS) detection and photothermal therapy (PTT) for single living cell analysis of epidermal growth factor receptor (EGFR) and specifically killed cancer cells with high EGFR expression. Additionally, to increase surface area, light-heat conversion efficiency and biocompatibility, we developed a silica coated nanoparticle conjugated with anti-human epidermal growth factor receptor 2 (HER2) antibody. Finally, three-dimensional TiO2 nanotubes with Au nanoparticles coating were synthesized and used to study trophoblast-derived stem-like cells growth on such 3D nanostructures.

The spread of invasive weeds continues to be a serious economic and environmental threat. Weed prevention has the potential to stop weeds before they become well established in an area conserving time, energy, and resources. Unfortunately, weed prevention is often overlooked. Weed Prevention Areas (WPAs) are a relatively new tool developed to help improve the application of weed prevention. They are cooperatively managed areas that focus on implementing prevention and early detection strategies at a community level. The purpose of this research was to establish baseline data that will be used to evaluate the overall effectiveness of the WPA concept, as well as to produce materials to assist individuals with the development of a WPA. Two rural communities, with new WPAs, were each paired with a non-WPA community for data collection purposes. On-the-ground GPS vegetation inventories were conducted to determine the initial abundance and distribution of selected invasive weed species. This information was then used to demonstrate how to prioritize species and sites within a WPA in order to utilize limited resources more efficiently. A mail-back survey was also conducted to evaluate landowners' current opinions and activities in regards to prevention and control. In general, weed prevention was viewed as an important part of integrated weed management, but fewer than half of all respondents applied prevention strategies on their property. The failure to implement prevention strategies was attributed to limited funding and resources, a lack of weed prevention knowledge, and a high level of perceived risk. The knowledge gained from this research was then used to create Step-By-Step Guidelines for Establishing a Weed Prevention Area. These Guidelines provide interested individuals the resources necessary to successfully organize a WPA in their community. In addition, four wildland weed mapping methods were evaluated to identify their strengths and weaknesses. There was no difference in the estimation of patch size or location between the buffered point, screen-drawn, and perimeter walked methods. In most situations, time and distance factors favor the selection of either the buffered point or screen-drawn method. If patch shape is an important consideration, the perimeter-walked or buffered point method should be selected.

Doctor of Philosphy (PhD) / This thesis describes the work carried out during four treks, each over 10-11 days, from 1400m to 5000m in the Nepal Himalaya and further work performed during several two-night sojourns at the Barcroft Laboratory at 3800m on White Mountain in California, USA. Nineteen volunteers were studied during the treks in Nepal and seven volunteers were studied at White Mountain. All subjects were normal, healthy individuals who had not travelled to altitudes higher than 1000m in the previous twelve months. The aims of this research were to examine the effects on sleep, and the ventilatory patterns during sleep, of incremental increases in altitude by employing portable polysomnography to measure and record physiological signals. A further aim of this research was to examine the relationship between the ventilatory responses to hypoxia and hypercapnia, measured at sea level, and the development of periodic breathing during sleep at high altitude. In the final part of this thesis the possibility of preventing and treating Acute Mountain Sickness with non-invasive positive pressure ventilation while sleeping at high altitude was tested. Chapter 1 describes the background information on sleep, and breathing during sleep, at high altitudes. Most of these studies were performed in hypobaric chambers to simulate various high altitudes. One study measured sleep at high altitude after trekking, but there are no studies which systematically measure sleep and breathing throughout the whole trek. Breathing during sleep at high altitude and the physiological elements of the control of breathing (under normal/sea level conditions and under the hypobaric, hypoxic conditions present at high altitude) are described in this Chapter. The occurrence of Acute Mountain Sickness (AMS) in subjects who travel form near sea level to altitudes above 3000m is common but its pathophysiology not well understood. The background research into AMS and its treatment and prevention are also covered in Chapter 1. Chapter 2 describes the equipment and methods used in this research, including the polysomnographic equipment used to record sleep and breathing at sea level and the high altitude locations, the portable blood gas analyser used in Nepal and the equipment and methodology used to measure each individual’s ventilatory response to hypoxia and hypercapnia at sea level before ascent to the high altitude locations. Chapter 3 reports the findings on the changes to sleep at high altitude, with particular focus on changes in the amounts of total sleep, the duration of each sleep stage and its percentage of total sleep, and the number and causes of arousals from sleep that occurred during sleep at increasing altitudes. The lightest stage of sleep, Stage 1 non-rapid eye movement (NREM) sleep, was increased, as expected with increases in altitude, while the deeper stages of sleep (Stages 3 and 4 NREM sleep, also called slow wave sleep), were decreased. The increase in Stage 1 NREM in this research is in agreement with all previous findings. However, slow wave sleep, although decreased, was present in most of our subjects at all altitudes in Nepal; this finding is in contrast to most previous work, which has found a very marked reduction, even absence, of slow wave sleep at high altitude. Surprisingly, unlike experimental animal studies of chronic hypoxia, REM sleep was well maintained at all altitudes. Stage 2 NREM and REM sleep, total sleep time, sleep efficiency and spontaneous arousals were maintained at near sea level values. The total arousal index was increased with increasing altitude and this was due to the increasing severity of periodic breathing as altitude increased. An interesting finding of this research was that fewer than half the periodic breathing apneas and hypopneas resulted in arousal from sleep. There was a minor degree of upper airway obstruction in some subjects at sea level but this was almost resolved by 3500m. Chapter 4 reports the findings on the effects on breathing during sleep of the progressive increase of altitude, in particular the occurrence of periodic breathing. This Chapter also reports the results of changes to arterial blood gases as subjects ascended to higher altitudes. As expected, arterial blood gases were markedly altered at even the lowest altitude in Nepal (1400m) and this change became more pronounced at each new, higher altitude. Most subjects developed periodic breathing at high altitude but there was a wide variability between subjects as well as variability in the degree of periodic breathing that individual subjects developed at different altitudes. Some subjects developed periodic breathing at even the lowest altitude and this increased with increasing altitude; other subjects developed periodic breathing at one or two altitudes, while four subjects did not develop periodic breathing at any altitude. Ventilatory responses to hypoxia and hypercapnia, measured at sea level before departure to high altitude, was not significantly related to the development of periodic breathing when the group was analysed as a whole. However, when the subjects were grouped according to the steepness of their ventilatory response slopes, there was a pattern of higher amounts of periodic breathing in subjects with steeper ventilatory responses. Chapter 5 reports the findings of an experimental study carried out in the University of California, San Diego, Barcroft Laboratory on White Mountain in California. Seven subjects drove from sea level to 3800m in one day and stayed at this altitude for two nights. On one of the nights the subjects slept using a non-invasive positive pressure device via a face mask and this was found to significantly improve the sleeping oxyhemoglobin saturation. The use of the device was also found to eliminate the symptoms of Acute Mountain Sickness, as measured by the Lake Louise scoring system. This finding appears to confirm the hypothesis that lower oxygen saturation, particularly during sleep, is strongly correlated to the development of Acute Mountain Sickness and may represent a new treatment and prevention strategy for this very common high altitude disorder.

Thesis (M.S. zoology)--Washington State University, December 2007. / Includes bibliographical references (p. 24-26).

L'hypoventilation alvéolaire chronique est considérée comme un marqueur d'évolution péjorative de différentes pathologies respiratoires. Cependant, son rôle physiopathologique dans différentes dysfonctions systémiques n'a pas été étudié de manière convaincante. Cette thèse avait pour but d'investiguer les conséquences de l'hypoventilation alvéolaire modérée au cours de l'insuffisance respiratoire chronique restrictive et les effets de son traitement par ventilation non-invasive.<br /> Nous avons montré que des patients affectés d'un syndrome obésité-hypoventilation (SOH) avaient une fonction endothéliale plus sévèrement altérée et une inflammation systémique plus importante que les patients obèses simples. La PaCO2 était corrélée à la dysfonction endothéliale (Borel et coll, manuscrit en préparation). Nous avons observé que la proportion d'hypoventilation en sommeil paradoxal, chez les sujets SOH, était associée à une réponse ventilatoire au CO2 abaissée et une somnolence diurne excessive. Pour la première fois, nous avons constaté que la ventilation non invasive nocturne améliorait la vigilance diurne objective (Chouri-Pontarollo et coll, Chest 2007). Nous menons actuellement la première étude randomisée du traitement des patients porteurs d'un SOH par VNI versus observation pendant un mois. L'analyse intermédiaire montrait qu'un mois de VNI nocturne chez les patients SOH améliorait la PaCO2 diurne, la capacité pulmonaire totale, la structure du sommeil, cependant aucun paramètre cardiovasculaire et métabolique n'était modifié. <br />Chez des patients insuffisants respiratoires chroniques pariéto-restrictifs, la VNI utilisée au cours d'un exercice aigu, augmentait la ventilation et améliorait la tolérance à l'effort (Borel et coll, Resp Med 2008). Chez ces mêmes patients, un réentrainement à l'effort sous VNI n'apportait pas de bénéfices additionnels par rapport à un réentrainement en ventilation spontanée sauf chez les patients les plus sévères. Ces derniers, amélioraient leur périmètre de marche et leur qualité de vie. Leur fatigue en particulier était améliorée s'ils s'étaient réentraînés sous VNI (Borel et coll, Am Journal of physical med and rehab, 2008, soumis). <br />Enfin, nous avons analysé l'impact des fuites intentionnelles des masques de VNI sur la performance des appareils de VNI bi-pressionnels. L'augmentation des fuites intentionnelles diminuait les capacités des appareils à atteindre et maintenir la pression de consigne. Ceci pouvait conduire à une diminution du volume délivré au patient, en particulier pour des fuites intentionnelles supérieures à 40 L.min-1 à 14 cm H2O de pression (Borel et al, Chest, sous presse). <br /> Conclusion : L'hypoventilation alvéolaire chronique peut-être considéré comme un déterminant physiopathologique de la dysfonction endothéliale, de l'inflammation, de la somnolence, et de l'intolérance à l'effort. La VNI, utilisée au cours des efforts, permet d'améliorer les capacités d'exercice et la qualité de vie des patients insuffisants respiratoires restrictifs les plus sévères. Malgré les limites technologiques des appareils de VNI bi-pressionnels utilisés actuellement, la VNI corrige l'hypoventilation alvéolaire des patients SOH, cependant les effets sur l'inflammation, la dysfonction endothéliale restent incertains à cours et long terme chez ces sujets obèses.

Mettre en oeuvre un retour d'effort pour un système robotique dédié à la chirurgie mini-invasive impose d'adresser deux difficultés principales. La première est d'ordre métrologique, puisqu'il est technologiquement très difficile de procéder à une mesure directe de l'interaction distale à l'intérieur du patient, tout en respectant les contraintes de stérilité et d'encombrement. La seconde concerne le contrôle d'interactions dont la géométrie et la dynamique sont fortement variables et mal connues (contacts avec des organes, le chirurgien, ou d'autres instruments) dans un contexte particulier où la contrainte cinématique induite par le passage des instruments par un point fixe ne permet pas l'asservissement de toutes les composantes du torseur d'interaction.<br />La réponse apportée à ces questions prend ici la forme d'un système robotique bâti autour :<br />- d'un bras compact de cinématique sphérique ;<br />- d'un capteur d'efforts placé à l'extérieur du patient permettant une estimation fine des interactions distales ;<br />- d'une commande en effort dont la passivité est garantie pour toutes les interactions ; celle-ci est déclinée selon plusieurs modes (retour explicite, commande en impédance, téléopération à retour d'efforts).<br /><br />L'ensemble des propositions méthodologiques est validé de façon systématique sur un prototype de laboratoire développé dans le cadre de ce travail. Les expériences incluent des validations in vivo sur animal, depuis des tâches élémentaires jusqu'à l'utilisation du prototype comme "main gauche" pour une opération de cholécystectomie.