Shigella flexneri is a Gram negative facultative anaerobe that infects millions world-wide each year. The route for infection of a host is through the intestinal and rectal epithelium layers, but it also can survive in the environment. Different genes have been found to be up regulated depending upon its presence in the intracellular or extracellular environment, as shown in previous work in the lab. This thesis seeks to examine the role these upregulated genes, bioA and lysA, play in the intracellular activity of S. flexneri. Knock-out mutations in the bioA and lysA genes were created using P1 transduction. To test the effects of these mutations on S. flexneri, plaque, invasion, and attachment assays were performed. It was found that the bioA mutation resulted in fewer plaques being formed, while the lysA mutation resulted in slower forming and incompletely lysed plaques being formed. / text

Security protocols are important and widely used because they enable secure communication to take place over insecure networks. Over the years numerous formal methods have been developed to assist protocol designers by analysing models of these protocols to determine their security properties. Beyond the design stage however, developers rarely employ formal methods when implementing security protocols. This may result in implementation flaws often leading to security breaches. This dissertation contributes to the study of security protocol analysis by advancing the emerging field of implementation analysis. Two tools are presented which together translate between Java and the LySa process calculus. Elyjah translates Java implementations into formal models in LySa. In contrast, Hajyle generates Java implementations from LySa models. These tools and the accompanying LySa verification tool perform rapid static analysis and have been integrated into the Eclipse Development Environment. The speed of the static analysis allows these tools to be used at compile-time without disrupting a developer’s workflow. This allows us to position this work in the domain of practical software tools supporting working developers. As many of these developers may be unfamiliar with modelling security protocols a suite of tools for the LySa process calculus is also provided. These tools are designed to make LySa models easier to understand and manipulate. Additional tools are provided for performance modelling of security protocols. These allow both the designer and the implementor to predict and analyse the overall time taken for a protocol run to complete. Elyjah was among the very first tools to provide a method of translating between implementation and formal model, and the first to use either Java for the implementation language or LySa for the modelling language. To the best of our knowledge, the combination of Elyjah and Hajyle represents the first and so far only system which provides translation from both code to model and back again.

The introductory chapter fills a completely blank space concerning the history, organisation and spirituality of the Order of the Discalced Augustinians in the Czech context. The existing literature has so far only briefly outlined this topic; however, it cannot be explored with no knowledge of the 20th -century professional Italian research works or the preserved resources produced by the General Curia in Rome and the 18th century literature of the Order. The thesis also provides a general overview of the activities of the Czech mon­ asteries of the Discalced Augustinians in the period context, also reflecting the in­ fluence of the Order on the spiritual and cultural life of the laymen, an influence which, as regards the monastery in Lnare, extends into the early 20th century. The extant resources have helped to describe relations between the members of the Order and the outside world, be it the links to the local clergy or laymen, espe­ cially burghers and nobility or its dependants. The relationship between the famil­ ies who financed the foundation of the two latest monasteries (Lnare and Lysa nad Labem) and the monastic community is the focus of specific attention. The monas­ tery benefactors who financed specific artworks were also recruited from these contacts. In return, they could hope to be...