The difference of Being in the early modern world: a relational-material approach to life in Scotland in the period of the witch trials

This thesis investigates how ways of being in different ontologies emerge from material and embodied practice. This general concern is explored through the particular case study of Scotland in the period of the witch trials (the 16th and 17th centuries C.E.). The field of early modern Scottish witchcraft studies has been active and dynamic over the past 15 years but its prioritisation of what people said over what they did leaves a clear gap for a situated and relational approach focusing upon materiality. Such an approach requires a move away from the Cartesian dichotomies of modern ontology to recognise past beliefs as real to those who experienced them, coconstitutive of embodiment and of the material worlds people inhabited. In theory, method and practice, this demands a different way of exploring past worlds to avoid flattening strange data. To this end, the study incorporates narratives and ‘disruptions’ – unique engagements with Contemporary Art which facilitate understanding by enabling the temporary suspension of disbelief. The methodology is iterative, tacking between material and written sources in order to better understand the heterogeneous assemblages of early modern (counter-) witchcraft. Previously separate areas of discourse are (re-)constituted into alternative ontic categories of newly-parallel materials. New interpretations of things, places, bodies and personhoods emerge, raising questions about early modern experiences of the world. Three thematic chapters explore different sets of collaborative agencies as they entwine into new things, co-fabricating a very different world. Moving between witch trial accounts, healing wells, infant burial grounds, animals, discipline artefacts and charms, the boundaries of all prove highly permeable. People, cloth and place bleed into one another through contact; trees and water emerge as powerful agents of magical-place-making; and people and animals meet to become single, hybrid-persons spread over two bodies. Life and death consistently emerge as protracted processes with the capacity to overlap and occur simultaneously in problematic ways. The research presented in this thesis establishes a new way of looking at the nature of Being as experienced by early modern Scots. This provides a foundation for further studies, which can draw in other materials not explored here such as communion wares and metal charms. Comparison with other early modern Western societies may also prove fruitful. Furthermore, the methodology may be suitable for application to other interdisciplinary projects incorporating historical and material evidence.

Metabolomics as a tool to explore the staphylococcal biofilm

Orthopaedic infections can be polymicrobial existing as a microbiome. Infections often incorporate staphylococcal species, including Staphylococcus aureus. Such infections can lead to life threatening illness and implant failure. Furthermore, biofilm formation on the implant surface can occur, increasing pathogenicity, exacerbating antibiotic resistance and altering antimicrobial mechanism of action. Bacteria change dramatically during the transition to a biofilm growth state: phenotypically; transcriptionally; and metabolically, highlighting the need for research into molecular mechanisms involved in biofilm formation. Metabolomics can provide a tool to analyse metabolic changes which are directly related to the expressed phenotype. Here, we aimed to provide greater understanding of orthopaedic infection caused by S. aureus and biofilm formation on the implant surface. Through metagenome analysis by employing: implant material extraction; DNA extraction; microbial enrichment; and whole genome sequencing, we present a microbiome study of the infected prosthesis to resolve the causative species of orthopaedic hip infection. Results highlight the presence of S. aureus as a primary cause of orthopaedic infection along with Enterococcus faecium and the presence of secondary pathogen Clostridium difficile. Although results were hindered by the presence of host contaminating DNA even after microbial enrichment, conclusions could be made over the potential increased pathogenicity caused by the presence of a secondary pathogen and highlight method and sample preparation considerations when undertaking such a study. Following this finding, studies were focused on an orthopaedic clinical isolate of S. aureus and a metabolome extraction method for staphylococcal biofilms was developed using cell lysis through bead beating and solvent metabolome extraction. The method was found to be reproducible when coupled with liquid chromatography-mass spectrometry (LC-MS) and bioinformatics, allowing for the detection of significant changes in metabolism between planktonic and biofilm cultures to be identified and drug mechanism of actions (MOA) to be studied. Metabolomics results highlight significant changes in a number of metabolic pathways including arginine biosynthesis and purine metabolism between the two cell populations, evidence of S. aureus responding to their changing environment, including oxygen availability and a decrease in pH. Focused investigations on purine metabolism looking for biofilm modulation effects were carried out. Modulation of the S. aureus biofilm phenotype was observed through the addition of exogenous metabolites. Inosine increased biofilm biomass while formycin B, an inosine analogue, showed a dispersal effect and a potential synergistic effect in biofilm dispersal when coupled with gentamycin. Changes in metabolism between planktonic cells and biofilms highlight the requirement for antimicrobial testing to be carried out against planktonic cells and biofilms. Untargeted metabolomics was used to study the MOA of triclosan in S. aureus. The triclosan target and MOA in bacteria has already been characterised, however, questions remain over its effects in bacteria. Although the use of triclosan has come under increasing speculation, its full effects are still largely unknown. Results show that triclosan can induce a cascade of detrimental events in the cell metabolism including significant changes in amino acid metabolism, affecting planktonic cells and biofilms. Results and conclusions provide greater understanding of orthopaedic infections and specifically focus on the S. aureus biofilm, confirming S. aureus as a primary cause of orthopaedic infection and using metabolomic analysis to look at the changing state of metabolism between the different growth states. Metabolomics is a valuable tool for biofilm and drug MOA studies, helping understand orthopaedic infection and implant failure, providing crucial insight into the biochemistry of bacteria for the potential for inferences to be gained, such as the MOA of antimicrobials and the identification of novel metabolic drug targets.