Presented on the candidate's behalf by Professor Roy D. Sleator and Brigid Lucey, Department of Biological Sciences, Cork Institute of Technology, March 18th, 2018 in recognition of the published works of Alan Lucid which was deemed suitable to be posthumously awarded with a PhD.

Thesis Cork Institute of Technology, 2018.

Includes bibliographical references.

"The presented thesis is composed of published works on which Mr. Alan Lucid (deceased) contributed significantly (as outlined in the accompanying table and corroborated in letters of support from his co-authors). As a bioinformatician, Alan contributed significantly to the genomic analysis and characterisation of Campylobacter ureolyticus, at the time, a newly identified human bacterial pathogen (pages 5-21). This work represented the first whole genome analysis of two C. ureolyticus isolates, including the type strain. Comparative analysis, subtractive hybridisation and gene ontology searches revealed a high degree of heterogenicity between C. ureolyticus isolates, as well as identifying 106 putative virulence associated factors, 52 of which are predicted to be secreted. Alan also played a key role in the EU-FP7 project ClouDx-i, which focused on the genomic sequencing and bioinformatics analysis of bacterial agents linked to neonatal sepsis (pages 24-38). This work paved the way for the development of a rapid diagnostic test for the identification of these key pathogens. Alan's work also helped to determine the role of the C-terminal coiled coil of the secondary proline proter ProP in contributing to Cronobacter sakazakii osmotolerance (pages 37-42). This work appears to suggest that the C-terminal coiled coil domain tunes ProP at low osmolaity, whereas ProP transporters lacking the coiled coil domain are more active at a higher osmolality range. This work has potential for the development of novel control strategies, independent of antibiotics, for controlling the growth of C.sakazakii in infant formula. Finally, as outlined in pages 43-59, Alan performed a thorough analysis of the genomics of the Weissella cibario strain (a genus of lactic acid bateria (LAB)). Analysis of four W. cibaria genomes indicated that the core-proteome, consisting of 729 proteins, constitutes 69% of the species pan-proteome. This large core-set may explain the divergent niches in which this species has been found. The presented papers represent just a fraction of Alan Lucid's contribution to our lab, nonetheless, in our opinion, they provide a convincing argument as to Alan's suitability to be posthumously awarded with a PhD". Abstract.