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The work presented in this thesis describes the X-ray crystallographic studies of particulatemethane monoxygenase (pMMO) from Methylococcus capsulatus (Bath), thioredoxin A(BsTrxA) from Bacillus subtilis and arginine decarboxylase (AdiA) from Escherichia coli.1. pMMO is a respiratory enzyme that catalyses the first step in the metabolic pathway inmethanotrophic bacteria by converting methane to methanol. The crystal structure of thisintegral membrane protein was determined by molecular replacement to 3.5 ? resolution. The three metal sites in pMMO were confirmed to be a mononuclear copper site, adinuclear copper site and a mononuclear zinc site.2. Thioredoxin is a ubiquitous protein present in nearly all known organisms. Its purposein the cell is to maintain cysteine-containing proteins in the reduced state by convertingintramolecular disulfide bonds to dithiols in a redox reaction. The crystal structure of anactive site mutant of BsTrxA was determined by molecular replacement to 1.5 ?resolution. The structure shows a homodimer that resembles enzyme-substrate reactionintermediates.3. AdiA is a vitamin B6-dependent enzyme that catalyses the decarboxylation of arginineinto agmatine. It forms a part of an enzymatic system in E. coli that contribute to makingthis organism acid resistant. The structure of arginine decarboxylase (AdiA) from E. coliwas determined by multiple isomorphous replacement and anomalous scattering (MIRAS)methods to 2.4 ? resolution. The structure revealed a ~800 kDa decamer composed as apentamer of five homodimers. AdiA becomes active as the cellular environment becomesmore acidic. The structure of AdiA suggests how functional decamers associate withdecreasing pH or disassociates into inactive homodimers with increasing pH. The enzymemechanism and determinants for substrate specificity are discussed within the frameworkof the structure and comparisons with related structures are made.

The mucosal immunity of the gastrointestinal (GI) tract is constituted by a complex, highly specialized and dynamic system of immune components that aim to protect the gut from external threats. The sustained exposure of the mucosal immune system of the GI tract to an enormous number of lumen antigens, requires the constant upkeep of a highly regulated balance between initiation of immune responses against harmful agents and the generation of immune tolerance towards innocuous antigens. Therefore, the regulatory component is key to preserve tissue homeostasis and a normal functioning of the system. Indeed, defective regulatory responses lead to the development of pathological conditions, including unresolved infections, and inflammatory diseases. In this study, we aim to elucidate novel mechanisms involved in host-pathogen interactions during Helicobacter pylori and Clostridium difficile infections. Indeed, this work integrates preclinical in vivo and in vitro experimental approaches together with a bioinformatics pipeline to identify and characterize novel regulatory mechanisms and molecular targets of the mucosal immune system during enteric infections. Firstly, we identified a novel regulatory mechanism during H. pylori infection mediated by a specific subset of IL10-producing tissue resident macrophages. Secondly, we employed an ex vivo H. pylori co-culture with bone marrow derived macrophages, that together with a global transcriptomic analysis and a bioinformatics pipeline, lead to the discovery of promising regulatory genes based on expression kinetics. Lastly, we characterized the innate inflammatory responses induced during the course of C. difficile infection and identified IL-1ß, and its subsequent induction of neutrophil recruitment, as a key mediator of C. difficile-induced effectors responses. The characterized regulatory mechanisms in this work show promise to lead the generation of new host-centered therapeutics through the modulation of the immune response as promising alternative treatments for infectious diseases.

This thesis is a study of the Islamist discourse on terrorism and how western countries are constructed in four Indonesian magazines, Tempo, Gatra, Sabili and SuaraHidayatullah, in relation to the five bombings which took place in Indonesia. I define the first two magazines as the general magazines and the last two as the Islamist magazines. The bombings coverage analysed is that of the Bali bombings 1 and 2, the JW Marriott 1 bombing, the Australian Embassy bombing and the JW Marriott 2/Ritz Carlton bombing. The first study is of the bomb which killed or injured more than 200 people in Kuta, Bali, an area which attracts large numbers of international tourists; the second is of the bomb which exploded in Jimbaran,Bali, also a tourist area; and the last three studies are of the bombings of icons of ‘the West.’ In addition, the way in which the readers of the magazines responded to the reporting of the five bombings analysed is also examined. To address the topic, I conducted research in the offices of four magazines in Jakarta. I copied articles from the Gatra, Sabili and Suara Hidayatullah offices, and Tempo provided me with digital copies. I also interviewed two or three journalists/editors from each magazine. Further, I conducted focus group discussions for the readers of the magazines. Ten focus groups were involved during the fieldwork. There were two groups for each magazine and the other two groups involved readers of both the general and Islamist magazines. The examination of the two general magazines shows that each constructs a different anti-western Islamist discourse in its reports on the terrorism. Gatra, in part, presents the Islamist view and construct that western countries are opposed to Islam, and therefore conspiracy theories concerning who was responsible for the bombings are likely to be true. Tempo, on the other hand, does not present an anti-western Islamist view in its reports. Mainstream views of terrorism are dominant. The comparison of the Islamist magazines shows a similarity in how the Islamists construct anti-western Islamist discourse in their reports. Both Sabili and Suara Hidayatullah view the western countries, mainly the United States, as anti-Islam and as enemies who would try to destroy and undermine Islam. The readers of the magazines generally perceive terrorism in Indonesia from an Islamist perspective, although they do not agree with acts of violence. The readers of both the general and Islamist magazines perceive the western countries (particularly the United States) as being in opposition to Islam and Muslims. The bombings which occurred in Indonesia are viewed with the suspicion that the western countries were involved. These findings show, partly, the Islamisation of society in the social and political context in contemporary Indonesia. They show not only that Islamisation exists in society (as exemplified by the readers), but that, to some extent, the media institution also has been Islamised. In the reform era, the Islamist magazines have the space and opportunity to disseminate their Islamist ideas, while the general magazines, though adopting mainstream views, are also partly Islamised by the strengthening of the journalists’ self-identification as Muslims.

Wetland mitigation is the practice of avoiding, minimizing or compensating for wetland functions and values lost through human impacts (e.g., filling). Regulated by the Army Corps of Engineers (Corps) and the Environmental Protection Agency through Section 404 of the Clean Water Act, wetland mitigation has become common in the last several decades. The goal of this project was to review wetland mitigation in South Dakota by 1) reviewing federal and state wetland policies and regulations; 2) examining the outcomes of wetland impact pennit requests completed and submitted to the South Dakota Corps Regulatory Office from 1996 to 1999; and 3) comparing the biodiversity among restored, created, enhanced and natural wetlands in eastern South Dakota. Almost 500 Section 404 permit applications were submitted in South Dakota from 1996 through 1999. All eligible applications were approved and nearly half of the permits issued included a provision for compensatory mitigation. Overall, the Section 404 program in South Dakota had an estimated net gain in wetland area of 272.75 ha. Although most permits issued were for the private sector, state agencies impacted more wetland area than other applicants. Many permits were from the South Dakota Department of Transportation and municipal highway departments; road projects were the most commonly named reason for wetland impacts (21. l % of permits issued). Projects involving water drainage and wetland restoration or creation resulted in the largest wetland area gains. Nationwide general permits were prevalent in all aspects of the study. The permit review indicated that Section 404 might successfully protect South Dakota wetlands. I used a rapid biodiversity assessment method to count birds, fish, mammals, amphibians and reptiles, and aquatic invertebrates using 17 compensatory mitigation and natural wetlands in eastern South Dakota. Wetlands were sampled twice each summer in 1999 and 2000. I determined few statistically or biologically significant differences in biodiversity among wetland types or sample periods in eastern South Dakota wetlands. Aquatic invertebrate taxa richness was significantly different among some wetland types (F=3.54, df=3, P=0.0268); there were more invertebrate taxa in restored than in created or enhanced wetlands and in natural wetlands than in created wetlands. Though not statistically significant, there appeared to be more bird species in restored than other wetland types and more fish species in created than natural wetlands. The similarities among wetland types for several animal groups indicate that each type of compensatory wetland will provide biodiversity comparable to one another and natural wetlands. These findings disagree with studies in other regions that showed limited success of compensatory mitigation wetlands. However, from studies of restored and created prairie wetlands not used for mitigation, it is clear that these techniques are effective in this region.