Sedimentation buildup and accumulation can cause serious impediments to the hydraulic capacity of culvert systems. There has not been any significant research to date regarding the behavior of bed load transport nor the implications of bed forms upon the hydraulics associated with culvert flow. The primary objective of this study was to investigate how sediment transport occurs in a culvert and to then develop a methodology and test setup to successfully investigate this sediment transport. The investigation was limited to studying culvert and pipeline transport of alluvial material in sand and gravel sizes. This dissertation develops a semi-empirical bed load transport equation from existing open channel flow models to be used in predicting sediment yields in culvert applications. Incipient motion and critical shear stresses were investigated for application into eight empirically based models. The methods analyzed include the Meyer-Peter Müller, Engelund and Hansen, Shields, Toffaleti (as seen in the United States Army Corps of Engineers program HEC RAS), Schoklitsch, DuBoy, Yang, and Rottner methods. These methods were tested for predictive accuracy to physically modeled bed load transport data obtained from a 304.8 mm (11.89 in) diameter culvert. Tests involved fully pressurized, partially pressurized inlet controlled, and open channel flow regimes for a variety of bed elevations and bedforms. Bedform regime and associated resistance impacts on flow energy were presented to better understand their hydraulic consequence in culvert applications. An extensive literature review regarding sediment transport in both open channel and closed conduit applications is provided to develop a foundation of knowledge to pursue further research in this area. This literature review summarizes the current body of scientific knowledge that is applicable to sediment transport in culverts. Investigations into both historical and current works are cited throughout this studies literature review. A tested methodology is presented for the investigation of sediment bed load transport in culvert applications. Development of a procedure for the testing of critical shear limits and bed load transport is outlined. A detailed application example is provided. Recommended changes in testing techniques and physical model are made for the next generation of culvert sediment transport research.

abstract: This study was devised to elucidate key information concerning the potential risk posed by Legionella in reclaimed water. A series of biological experiments and a recharge basin soil column study were conducted to examine the survival, growth, and transport of L. pneumophila through engineered reclaimed water systems. A pilot-scale, column study was set up to measure Legionella transport in the columns under Arizona recharge basin conditions. Two columns, A and B, were packed to a depth of 122 cm with a loamy sand media collected from a recharge basin in Mesa, Arizona. The grain size distribution of Column A differed from that of Column B by the removal of fines passing the #200 sieve. The different soil profiles represented by column A and B allowed for further investigation of soil attributes which influence the microbial transport mechanism. Both clear PVC columns stand at a height of 1.83 m with an inner diameter of 6.35 cm. Sampling ports were drilled into the column at the soil depths 15, 30, 60, 92, 122 cm. Both columns were acclimated with tertiary treated waste water and set to a flow rate of approximately 1.5 m/d. The columns were used to assess the transport of a bacterial indicator, E. coli, in addition to assessing the study's primary pathogen of concern, Legionella. Approximately, 〖10〗^7 to 〖10〗^9 E. coli cells or 〖10〗^6 to 〖10〗^7Legionella cells were spiked into the columns' head waters for each experiment. Periodically, samples were collected from each column's sampling ports, until a minimum of three pore volume passed through the columns. The pilot-scale, column study produced novel results which demonstrated the mechanism for Legionella to be transported through recharge basin soil. E. coli was transported, through 122 cm of the media in under 6 hours, whereas, Legionella was transported, through the same distance, in under 30 hours. Legionella has been shown to survive in low nutrient conditions for over a year. Given the novel results of this proof of concept study, a claim can be made for the transport of Legionella into groundwater aquifers through engineering recharge basin conditions, in Central Arizona. / Dissertation/Thesis / Masters Thesis Civil and Environmental Engineering 2014

L’introduction commence avec la description de toxines d’origines bactérienne et végétale, en particulier la toxine Shiga ainsi que les toxines de la même famille (chapitre 9.1.2). Les petites molécules inhibitrices de ces toxines sont ensuite résumées dans le chapitre 9.1.3, en particulier le composé Retro-2. L’efficacité de ces toxines à atteindre leurs cibles reposant sur le trafic intracellulaire, un aperçu général de l’endocytose et du trafic endosomal sont présentés (chapitre 9.2). Puis, l’entrée de la voie rétrograde est décrite (chapitre 9.2.5), avec un intérêt particulier porté sur la clathrine, le rétromère et GPP130, une protéine qui circule de manière continue entre le Golgi, la membrane plasmique et les endosomes. Les protéines SNARE, en particulier la syntaxine-5 et le syntaxine-16, sont ensuite introduites (chapitre 9.2.6). Après une brève section sur les micro-ARNs de la famille 199 (chapitre 9.3), l’introduction se termine avec la description des techniques clés utilisées au cours de mon travail, tels que la chimie click bio-orthogonale, la synchronisation du trafic antérograde par rétention grâce à des hameçons spécifiques (RUSH), et la ligation par proximité basé sur des anticorps (chapitre 9.4).Ci-inclus, mon article en cours de soumission ouvre la partie résultats (chapitre 10.1), dans laquelle je présente l’intérêt de la chimie click bio-orthogonale pour identifier les cibles cellulaires de Retro-2. Je décris un des candidats potentiels, Sec16A, et illustre comment grâce à la technique de RUSH, perturber la fonction de Sec16A conduit à la relocalisation partielle de la syntaxin-5 au niveau du reticulum endoplasmique via l’inhibition du transport antérograde de la syntaxine-5. La seconde partie de l’article décrit comment la relocalisation de la syntaxine-5 induit l’inhibition du trafic de la toxine Shiga des endosomes au TGN. Je présente une nouvelle interaction entre la syntaxine-5 et la protéine TGN GPP130, qui ont déjà été caractérisées en relation avec le trafic de la toxine Shiga. Mon travail connecte à la fois les facteurs de trafic avec le trafic rétrograde au niveau de l’interface endosome-TGN. De manière frappante, cette interaction est très probablement basée sur une fonction non-SNARE de la syntaxine-5 car le domaine de fixation sur GPP130 est structurellement non lié à toute fonction SNARE.En collaboration avec Juan Francisco Aranda et Carlos Fernandez aux Etats-Unis, nous avons placés des micro-ARNs dans un contexte de régulation endogène du trafic rétrograde de la toxine Shiga (chapitre 11.2). Une discussion plus approfondie sera apportée dans le chapitre 12.Enfin, une vue d’ensemble des projets en cours est apportée dans la section des perspectives (chapitre 12), dans laquelle les collaborations plus approfondies sont mises en lumière.Mots clés : transport rétrograde, toxine Shiga, toxine de la famille Shiga, STxB, syntaxin-5, Sec16A, GPP130, Retro-2, Retro-2.1, chimie click sans cuivre, identification des cibles de petites molécules, spétrométrie de masse, function non-SNARE, inhibition du trafic antérograde, miARN, miR199, rétromère, VPS26 / The introduction of my PhD manuscript starts with describing plant and bacterial toxins (chapter 9.1), in particular Shiga toxin and Shiga-like toxins (SLTs) (chapter 9.1.2). Small molecule inhibitors of these toxins are summarized afterwards in chapter 9.1.3, notably the Retro-2 compound. Since these toxins rely on intracellular trafficking to reach their molecular targets, a general overview of endocytosis and endosomal trafficking is provided (chapter 9.2). Next, the retrograde route entry is presented (chapter 9.2.5), with focus on clathrin, the retromer and GPP130, a protein that constantly cycles between Golgi, plasma membrane, and endosomes. SNARE proteins, particularly syntaxin-5 and syntaxin-16, are then introduced (chapter 9.2.6). After a brief section of the micro RNA family 199 (chapter 9.3), the introduction finishes with the description of some salient techniques that were used in my work, such as - bio-orthogonal Click-Chemistry, anterograde trafficking synchronization with the retention using selective hooks (RUSH) assay, and the antibody-based proximity ligation assay (chapter 10.6.1, 0, 10.11.1).Herein, my submitted publication opens the results part (chapter 11.1), in which I present the utility of biorthogonal click chemistry for the search of the cellular targets of Retro-2, a small molecule inhibitor that was previously shown to protect cells and animals against Shiga toxin and ricin. I describe that Sec16A is a likely cellular target candidate, and illustrate using the RUSH approach how interfering with Sec16A functions leads to the partial relocalization of syntaxin-5 to the endoplasmic reticulum (ER) by slowing-down its anterograde transport. The second part of the paper describes how syntaxin-5 relocalization causes the inhibition of Shiga toxin trafficking from endosomes to the TGN. I present a novel interaction between syntaxin-5 and the Golgi protein GPP130, which both have been already described in relation to Shiga toxin trafficking. My work connects both trafficking factors in retrograde trafficking at the endosomes-TGN interface. Strikingly, I demonstrate that this interaction is most probably based on a non-SNARE function of syntaxin-5.In collaboration with Juan Francisco Aranda and Carlos Fernandez in the US, we put micro RNAs into an endogenous regulation context of Shiga toxin retrograde trafficking (chapter 11.2). An extended discussion will be given in chapter 12.Last, a general outlook of ongoing projects is given in the perspectives section (chapter 13), in which further collaborations are highlighted.Keywords: Retrograde transport, Shiga toxin, Shiga-like toxin (SLT), STxB, syntaxin-5, Sec16A, GPP130, Retro-2, Retro-2.1, azide-functionalized Retro-2, copper-free click chemistry, small molecule target identification, mass spectrometry, non-SNARE function, anterograde trafficking inhibition, miRNA, miR199, retromer, VPS26

Trasport Terminal