Using a multiple stage age of infection model, we derive an expression for the basic reproduction number, Ro. We apply this method to find Ro in analogous treatment models. We find, in the model without treatment, Ro depends only on the mean infective period, and not on the infective distribution. In treatment models, Ro depends on the mean infective and mean treatment period, as well as the distribution of the infective period, but not on the distribution of the treatment period. With an explicit formula for Ro and the final size relation, we provide a practical alternative to evaluating the effect of treatment and other control measures. We compare our models to previous models of SARS and TB.

Using a multiple stage age of infection model, we derive an expression for the basic reproduction number, Ro. We apply this method to find Ro in analogous treatment models. We find, in the model without treatment, Ro depends only on the mean infective period, and not on the infective distribution. In treatment models, Ro depends on the mean infective and mean treatment period, as well as the distribution of the infective period, but not on the distribution of the treatment period. With an explicit formula for Ro and the final size relation, we provide a practical alternative to evaluating the effect of treatment and other control measures. We compare our models to previous models of SARS and TB.

Using a multiple stage age of infection model, we derive an expression for the basic reproduction number, Ro. We apply this method to find Ro in analogous treatment models. We find, in the model without treatment, Ro depends only on the mean infective period, and not on the infective distribution. In treatment models, Ro depends on the mean infective and mean treatment period, as well as the distribution of the infective period, but not on the distribution of the treatment period. With an explicit formula for Ro and the final size relation, we provide a practical alternative to evaluating the effect of treatment and other control measures. We compare our models to previous models of SARS and TB. / Science, Faculty of / Mathematics, Department of / Graduate

In 2005 an equine rhinitis A virus (ERAV) isolate was recovered from a febrile horse during a respiratory outbreak in Ontario. This isolate (ERAV/ON/05) was propagated in cell culture and used to study its genomic characteristics and to investigate the clinical features in experimentally infected ponies. The fulllength genome of this isolate was sequenced and compared with other ERAV available in GenBank. The isolate genome is 7839 nucleotides (nts) in length with a variable 5’UTR and a more conserved 3’UTR. When the isolate was compared to other reported ERAV, an insertion of 13 nts in the 5’UTR was identified. Phylogenetic analysis demonstrated that ERAV/ON/05 was closely related to the ERAV/PERV isolate, which was recovered in 1962 in the United Kingdom. An experimental model was developed to study the clinical infection in naïve healthy ponies (ERAV/ON/05 n=4 and placebo n=4). ERAV/ON/05 induced clinical respiratory disease compared to placebo. The clinical signs consisted of pyrexia, nasal discharge, increased and abnormal lung sounds, increased size of submandibular lymph nodes and persistent mucopus in the trachea (up to 21 days post-infection). The virus was isolated from the lower and upper airways up to day 7 post-infection, corresponding with the detection of neutralizing ERAV antibodies. Assessment of the cytokine profile from bronchoalveolar lavage (BAL) cells demonstrated that this infection induced down-regulation of the mRNA expression of IL-4. One year later, four previously infected ponies with neutralizing antibodies to ERAV were assigned to a reinfection trial. None of the re-infected ponies developed clinical disease, and only one animal had a four-fold increase in antibody titres to ERAV. Attempts to recover the virus from the re-infected ponies using cell culture were negative; however, a down-regulation of the mRNA expression of IL-4 and IFN-β was identified in BAL cells. In conclusion, this study shows that the genome of ERAV has not significantly changed in the last 50 years and more importantly the virus induces clinical respiratory disease similar to other common equine respiratory viruses.

A general procedure is described for the analysis of gene expression of Candida albicans cultured in a mouse infection model. This technique involves first infecting mice with Candida and subsequently harvesting blood and other tissue at specific time points during infection. The tissues are homogenized and the infecting Candida isolated. Finally, RNA is extracted from recovered Candida cells and subjected to microarray analysis.

Master of Science / Department of Diagnostic Medicine/Pathobiology / Sanjeev K. Narayanan / Acute diarrhea induced by Escherichia coli is an important illness in humans, especially in children under age of two in developing countries. Citrobacter rodentium is used as murine model for E. coli infection in humans because it causes ultrastructural changes in murine colonic epithelium comparable to lesions produced by enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC). Adult mice of many strains develop self-limiting epithelial hyperplasia when infected, whereas adult C3H and FVB mice are highly susceptible to infection and demonstrate mortality rates between 60 and 100% two weeks after infection. These susceptible strains of mice also have higher bacterial translocation to mesenteric lymph nodes. In mice, the cause of death could be hypovolemia due to dehydration that may occur due to an increase in paracellular permeability as well as dysregulation of apical and basolateral ion transporting proteins. C. rodentium virulence factors resemble those of E. coli and are believed to primarily alter tight junctions of colonic epithelial cells. Effectors delivered via the type III secretory system have been associated with actin condensation and pedestal formation. The exact mechanisms of C. rodentium infection, as well as changes that occur in vitro as well as in the intestine of various strains of mice are not completely understood. This study introduced a new in vitro Ptk6 cell line for C. rodentium infection, which can also serve as a model for EPEC in humans. Effect of C. rodentium on colonic epithelial cells of susceptible and resistant mice was determined in in vivo study. C. rodentium attached to Ptk6 colonic epithelial cells, inducing attaching and effacing (A/E) lesions and loss of monolayer integrity, which charachterizes this cell line as a relevant in vitro model of C. rodentium and EPEC infections. Murine studies revealed that C. rodentium induced more severe disease and 100% mortality in juvenile C3H mice whereas Swiss Webster (SW) mice expressed only moderate morbidity. The colonic lesions and changes in barrier function of colonic epithelium were more prominent in C3H mice. This study determined potential targets in the murine colon that play role the establishment and the outcome of the infection, indicating multifactorial nature of C. rodentium-induced diarrhea. This study identified host factors involved in the initiation of C. rodentium-associated diarrhea and the outcome of infection, which can be useful in developing of novel strategies for preventing and treatment of infectious colitis.

Distributed Computing Infrastructures (DCIs) have emerged as a viable and affordable solution to the computing needs of communities of practice that may require the need to improve system performance or enhance the availability of their scientific applications. According to the literature, the ease of access and several other issues which relate to the interoperability among different resources are the biggest challenges surrounding the use of these infrastructures. The traditional method of using a Command Line Interface (CLI) to access these resources is difficult and can make the learning curve quite steep. This approach can result in the low uptake of DCIs as it prevents potential users of the infrastructures from adopting the technology. Science Gateways have emerged as a viable option that are used to realise the high-level scientific domain-specific user interfaces that hide all the details of the underlying infrastructures and expose only the science-specific aspects of the scientific applications to be executed in the various DCIs. A Science Gateway is a digital interface to advanced technologies which is used to provide adequate support for science and engineering research and education. The focus of this study therefore is to propose and implement a Methodology for dEveloping Scientific Software Applications in science GatEways (MESSAGE). This will be achieved by testing an approach which is considered to be appropriate for developing applications in Science Gateways. In the course of this study, several Science Gateway functionalities obtained from the review of literature which may be utilised to provide services for different communities of practice are highlighted. To implement the identified functionalities, this study utilises the methodology for developing scientific software applications in Science Gateways. In order to achieve this purpose, this research therefore adopts the Catania Science Gateway Framework (CSGF) and the Future Gateway approach to implement the methods and ideas described in the proposed methodology, as well the essential services of Science Gateways discussed throughout the thesis. In addition, three different set of scientific software applications are utilised for the implementation of the proposed methodology. While the first application primarily serves as the case study for implementing the methodology discussed in this thesis, a second application is used to evaluate the entire process. Furthermore, several other real-life scientific applications developed (using two distinctly different Science Gateway frameworks) are also utilised for the purpose of evaluation. Subsequently, a revised MESSAGE methodology for developing scientific software applications in Science Gateways is discussed in the latter Chapter of this thesis. Following from the implementation of both scientific software applications which sees the use of portlets to execute single experiments, a study was also conducted to investigate ways in which Science Gateways may be utilised for the execution of multiple experiments in a distributed environment. Finally, similar to making different scientific software applications accessible and available (worldwide) to the communities that need them, the processes involved in making their associated research outputs (such as data, software and results) easily accessible and readily available are also discussed. The main contribution of this thesis is the MESSAGE methodology for developing scientific software applications in Science Gateways. Other contributions which are also made in different aspects of this research include a framework of the essential services required in generic Science Gateways and an approach to developing and executing multiple experiments (via Science Gateway interfaces) within a distributed environment. To a lesser extent, this study also utilises the Open Access Document Repository (OADR) (and other related technologies) to demonstrate accessibility and availability of research outputs associated with specific scientific software applications, thereby introducing the concept (and thus laying the foundation) of an Open Science research.

Melioidosis is a neglected tropical disease that continues unabated in many countries, particularly in Southeast Asia. There is no vaccine and antimicrobial treatment is expensive and complicated. Virulence models are important tools used to investigate genes involved in pathogenesis. Galleria mellonella is the larvae of the wax worm moth that has been used to model various infections. Based on previous studies, we attempted to establish an infection model using Burkholderia pseudomallei and Burkholderia thailandensis, a related species which is avirulent in humans. Injections of various forms of these species (fresh and frozen) were used to develop Kaplan-Meier plots. We also tested Burkholderia cepacia, Burkholderia vietnamiensis, Burkholeria ambifaria, and Burkholderia multivorans to understand how they affect the larvae. We found that larvae injected with B. pseudomallei and B. thailandensis did not accurately model the respective infections these species cause in humans, while the other non-virulent species did not produce disease, as expected. We conclude that G. mellonella is not an appropriate infection model for B. pseudomallei and B. thailandensis. Healthcare-associated infections (HAI) are on the rise, and place a heavy burden on our healthcare system each year. Disinfectants used in healthcare settings can reduce HAIs, but first must be evaluated for proper efficacy. To date there are few statistical models that are useful in comparing disinfectant test methods. We conducted a head-to-head comparison of two common test methods, suspension and surface, using Clostridium difficile spores as the test organism. A novel statistical method was developed to evaluate which test method better predicted disinfectant performance. An activated disinfectant that gradually lost activity over time was used in these evaluations. Results showed that the suspension test method was less variable, and was a better predictor of disinfectant efficacy over time.

Einleitung: Toxoplasma (T.) gondii zählt zu den häufigsten intrazellulären Parasiten weltweit. Alleinige Endwirte im fakultativ heteroxenen Lebenszyklus sind die Feliden. Als Zwischenwirte können jedoch zahlreiche Säugetier- und Vogelarten dienen, in denen sich parasitäre Gewebezysten entwickeln. Einer der Hauptübertragungswege auf den Menschen stellt der Verzehr von T. gondii-haltigem Fleisch infizierter Nutztiere dar. Inwieweit Putenfleisch ein potentielles Infektionsrisiko birgt und welche Bedeutung Puten in der Epidemiologie der humanen Toxoplasmose besitzen ist nicht ausreichend geklärt. Ziel der Untersuchungen: Ziel der vorliegenden Arbeit war es, ein reproduzierbares Infektionsmodell bei Puten für T. gondii zu entwickeln, um die Verteilung und Persistenz des Parasiten im Gewebe zu ermitteln. Es wurden verschiedene Parameter, wie Infektionsstadium, Infektionsdosis, Applikationsmodus und Untersuchungszeitpunkt hinsichtlich ihres Einflusses auf die Entwicklung parasitärer Gewebestadien verglichen. Material und Methoden: Insgesamt wurden 74 Puten nach einer Aufzuchtperiode von 4 bis 8 Wochen experimentell mit T. gondii-Tachyzoiten oder Oozysten infiziert. Je nach Versuchsgruppe wurden Tachyzoiten vom Stamm ME49 intravenös und/oder intramuskulär appliziert oder Oozysten vom Stamm ME49, DX oder Hannover 1 oral verabreicht. Die Verifikation der Infektion erfolgte über den Nachweis T. gondii-spezifischer Antikörper mit Hilfe eines kinetischen ELISA. Drei bis acht Puten jeder Versuchsgruppe wurden 6 bis 8 oder 10 bis 12 Wochen nach der Infektion getötet. Von jedem Tier wurden folgende Gewebeproben entnommen: Brust-, Oberschenkel- und Unterschenkelmuskulatur, Herz, Leber, Muskel- und Drüsenmagen, Gehirn, Lunge, Milz, Nieren, Darm, Pankreas und Hoden (sofern vorhanden). Die Organe wurden getrennt vollständig homogenisiert. Bei den Muskeln wurden Proben von verschiedenen Lokalisationen entnommen und ebenfalls einzeln homogenisiert. Der Nachweis von T. gondii-DNA in den Gewebeproben erfolgte mittels konventioneller PCR, basierend auf der Amplifizierung eines 469 bp Fragments des B1-Gens, und anschließender nested PCR (Länge Zielfragment: 375 bp). Zusätzlich wurden zu Beginn der Studie lichtmikroskopische Untersuchungen einzelner Organe in Form nativer Quetschpräparate (400fache Vergrößerung) auf T. gondii-Zysten durchgeführt. Ergebnisse: Ungeachtet der Infektionsdosis und des inokulierten Parasitenstadiums konnten bei keinem der Versuchstiere klinische Symptome einer Toxoplasmose beobachtet werden. Die unterschiedlich hohen Infektionsdosen hatten im Allgemeinen keinen signifikanten Einfluss auf die Anzahl positiv getesteter Puten oder Organproben. Lediglich die Anzahl positiver Gehirnproben nahm mit ansteigender Oozystendosis signifikant zu. Bei der Betrachtung aller Versuchsgruppen fiel auf, dass die Befallshäufigkeit der Organe sowohl zwischen den Tieren verschiedener Infektionsgruppen als auch innerhalb einer Infektionsgruppe stark schwankte. So variierte die Anzahl positiv getesteter Organe bei den Tachyzoiten-infizierten Puten zwischen 0 und 7, bei den Oozysten-infizierten Puten zwischen 0 und 9 Organen pro Tier. Die Untersuchungsergebnisse zeigen, dass sich T. gondii heterogen in der Pute verteilt und mindestens 12 Wochen persistieren kann. Bezogen auf alle Versuchstiere gab es kein Organ, dass durchgängig negativ blieb. Nach der Tachyzoiteninfektion waren am häufigsten Leber (43,3%), gefolgt von Brustmuskel (26,7%) und Herz (20,0%) infiziert, während bei den Oozysten-infizierten Tieren der Erreger am häufigsten im Gehirn (47,2%), gefolgt von Oberschenkelmuskulatur (25,0%) und Herz und Unterschenkelmuskulatur (je 22,2%) nachgewiesen werden konnte. Schlussfolgerungen: Tachyzoiten und Oozysten erwiesen sich als gleichermaßen geeignete Infektionsmedien und führten hinsichtlich der systemischen Verteilung des Parasiten in der Pute zu vergleichbaren Ergebnissen. Ein spezifischer Organtropismus des Erregers konnte nicht festgestellt werden. Aus Sicht der Lebensmittelhygiene und des Verbraucherschutzes bedeuten die Ergebnisse, dass im Fall einer T. gondii-Infektion ein potentielles Infektionsrisiko für den Menschen durch infiziertes Putenfleisch nicht ausgeschlossen werden kann.

Plus de 150 années de recherches sur les Microsporidies ont conduit à une connaissance relativement basique de divers aspect de leur biologie. Malgré cela, peut d’informations existent concernant la génétique et les mécanismes moléculaire des interactions hôte-pathogène qui gouvernent les infections aux Microsporidies.Dans un premier temps, je décris comment détecter, traiter et éradiquer les infections microsporidiales avec Tubulinosema ratisbonensis dans des lignées de Drosophila melanogaster. Jusqu’à présent, les connaissances concernant les défenses de l’hôte chez la drosophile contre les parasites intracellulaire obligatoires restent incomplète due au manque d’un bon modèle d’infection. De ce fait, j’ai développé des modèles d’infection de D. melanogaster par la microsporidie T.ratisbonensis, à la fois en culture cellulaire et drosophiles adultes. Mes travaux sur le modèle d’infection cellulaire englobent des approchent en transcriptomique et métabolomique qui analysent les deux cotées de cette relation hôte-pathogène. En fin, je présente les fonctions biologiques des glycosylphosphatidyl inositoles de Toxoplasma gondii. / More than 150 years of Microsporidia research led to a basic understanding of many aspects of microsporidial biology, yet little is known about the genetic basis and molecular mechanisms of the intimate host-parasite relationship that govern Microsporidia infections.Here, I first report on the detection, prophylaxis, and eradication measures against microsporidial infestations with Tubulinosema ratisbonensis, infecting cultures of Drosophila melanogaster. To date,knowledge about Drosophila host defense against obligate intracellular parasites remained incomplete for lack of good infection models.To this end, I have developed infection models of Drosophila by the microsporidian T. ratisbonensis,both in cell lines and in adults. The work on the cellular infection model encompasses transcriptomics and metabolomics approaches, which aim to attempt both sides of the host-pathogen equation. Finally, I report on the biological roles of glycosylphosphatidyl inositols of Toxoplasma gondii.