A novel activation mechanism for Clostridial bacteriophage endolysins

Bacteriophage-encoded endolysins are produced at the end of the phage lytic cycle for the degradation of the host bacterial cell. Endolysins offer the potential as alternatives to antibiotics as biocontrol agents or therapeutics. The lytic mechanisms of three bacteriophage endolysins that target Clostridium species living under different conditions were investigated. For these endolysins a trigger and release mechanism is proposed for their activation. During host lysis, holin lesion formation suddenly permeabilises the membrane which exposes the cytosol-sequestered endolysins to a sudden environmental shock. This shock is suggested to trigger a conformational switch of the endolysins between two distinct dimer states. The switch between dimer states is proposed to activate a novel autocleavage mechanism that cleaves the linker connecting the N-terminal catalytic domain and the C-terminal domain to release the catalytic domain for more efficient digestion of the bacterial cell wall. Crystal structures of cleaved fragments of CD27L and CTP1L were previously obtained. In these structures cleavage occurs at the stem of the linker connected to the C-terminal domain. Despite a sequence identity of only 22% between 81 residues of the C-terminal domains of CD27L and CTP1L, they represent a novel fold that is identified in a number of different lysins. Within the crystal structures the two distinct dimerization modes are represented: the elongated head‐on dimer and the side-by‐side dimer. Introducing mutations that inhibit either of the dimerization states caused a decrease in the efficiency of both the autocleavage mechanism and the lytic activity of the endolysins. The two dimer states were validated for the full-length endolysins in solution by using right angle light scattering, small angle X‐ray scattering and cross-linking experiments. Overall, the data represents a new type of regulation governed by the C-terminal domains that is used to activate these endolysins once they enter the bacterial cell wall.

Small angle scattering characterisation of micellar systems and templated architectures

The work described in this thesis reports the structural changes induced on micelles under a variety of conditions. The micelles of a liquid crystal film and dilute solutions of micelles were subjected to high pressure CO2 and selected hydrocarbon environments. Using small angle neutron scattering (SANS) techniques the spacing between liquid crystal micelles was measured in-situ. The liquid crystals studied were templated from different surfactants with varying structural characteristics. Micelles of a dilute surfactant solution were also subjected to elevated pressures of varying gas atmospheres. Detailed modelling of the in-situ SANS experiments revealed information of the size and shape of the micelles at a number of different pressures. Also reported in this thesis is the characterisation of mesoporous materials in the confined channels of larger porous materials. Periodic mesoporous organosilicas (PMOs) were synthesised within the channels of anodic alumina membranes (AAM) under different conditions, including drying rates and precursor concentrations. In-situ small angle x-ray scattering (SAXS) and transmission electron microscopy (TEM) was used to determine the pore morphology of the PMO within the AAM channels. PMO materials were also used as templates in the deposition of gold nanoparticles and subsequently used in the synthesis of germanium nanostructures. Polymer thin films were also employed as templates for the directed deposition of gold nanoparticles which were again used as seeds for the production of germanium nanostructures. A supercritical CO2 (sc-CO2) technique was successfully used during the production of the germanium nanostructures.

The right to humanitarian assistance in natural and human-made disasters: progress and challenges for an emerging international legal framework

Natural and human-made disasters cause on average 120,000 deaths and over US$140 billion in damage to property and infrastructure every year, with national, regional and international actors consistently responding to the humanitarian imperative to alleviate suffering wherever it may be found. Despite various attempts to codify international disaster laws since the 1920s, a right to humanitarian assistance remains contested, reflecting concerns regarding the relative importance of state sovereignty vis-à-vis individual rights under international law. However, the evolving acquis humanitaire of binding and non-binding normative standards for responses to humanitarian crises highlights the increasing focus on rights and responsibilities applicable in disasters; although the International Law Commission has also noted the difficulty of identifying lex lata and lex ferenda regarding the protection of persons in the event of disasters due to the “amorphous state of the law relating to international disaster response.” Therefore, using the conceptual framework of transnational legal process, this thesis analyses the evolving normative frameworks and standards for rights-holders and duty-bearers in disasters. Determining the process whereby rights are created and evolve, and their potential internalisation into domestic law and policy, provides a powerful analytical framework for examining the progress and challenges of developing accountable responses to major disasters.

“Something isn’t right here”: American exceptionalism and the creative nonfiction of the Vietnam War

In this thesis, I argue that few attempts were as effective in correcting the exceptionalist ethos of the United States than the creative nonfiction written by the veterans and journalists of the Vietnam War. Using critical works on creative nonfiction, I identify the characteristics of the genre that allowed Paul John Eakin to call it ‘a special kind of fiction.’ I summarise a brief history of creative nonfiction to demonstrate how it became a distinctly American form despite its Old World origins. I then claim that it was the genre most suited to the kind of ideological transformation that many hoped to instigate in U.S. society in the aftermath of Vietnam. Following this, the study explores how this “new” myth-making process occurred. I use Tim O’Brien’s If I Die in a Combat Zone and Philip Caputo’s A Rumor of War to illustrate how autobiography/memoir was able to demonstrate the detrimental effect that America’s exceptionalist ideology was having on its population. Utilising narrative and autobiographical theory, I contend that these accounts represented a collective voice which spoke for all Americans in the years after Vietnam. Using Neil Sheehan’s A Bright Shining Lie and C.D.B. Bryan’s Friendly Fire, I illustrate how literary journalism highlighted the hubris of the American government. I contend that while poiesis is an integral attribute of creative nonfiction, by the inclusion of extraneous bibliographic material, authors of the genre could also be seen as creating a literary context predisposing the reader towards an empirical interpretation of the events documented within. Finally, I claim that oral histories were in their essence a synthesis of “everyman” experiences very much in keeping with the American zeitgeist of the early Eighties. Focussing solely on Al Santoli’s Everything We Had, I demonstrate how such polyphonic narratives personalised the history of the Vietnam War.