Fixed-term

OVERVIEW Humectants are used by the food industry for numerous reasons, such as the use of salt as flavour enhancing ingredient. They are most commonly used to reduce the moisture content of a food matrix, leading to a more stable product with a longer shelf life. Ultimately the aim is to reduce the incidence of foodborne illness. However, as consumer concern over the increased risk of detrimental health effects resulting from the over-intake of NaCl, food producers need to explore alternative humectants that can be utilised. Two of these are KCl and glycerol. Salmonella have been shown to survive for extended periods of time in numerous low-moisture products such as chocolate and peanut butter. Previous work has identified the minimum bactericidal concentrations of NaCl, KCl and glycerol towards a panel of Salmonella isolates. Other work has examined the effect of heat resistance post habituation within these compounds, and identified several genes up-regulated in response to NaCl shock. However, information is lacking regarding the transcriptomic responses towards KCl and glycerol humectants. The aim of this study is to compare the response of the model organism Salmonella Typhimurium ST4/74 to sub-inhibitory concentrations of NaCl, KCl and glycerol to understand the mechanisms utilised to sustain viability. Using deep-level RNA sequencing (RNA-seq) the experiment will also allow direct comparison of the responses observed within all three conditions. It is hypothesised that genes involved in sustaining viability at sub-inhibitory levels will also prove important to survival within high concentrations of the humectants. To test this hypothesis, deletion mutants will be created based on genes identified by transcriptomic studies, and viability measured in comparison to the wild-type under a range of humectant concentrations. As recovery of viable cells from high levels of humectants has been shown to be difficult using traditional culture techniques, we propose the use of flow cytometry for the enumeration of cells exposed to humectant stress. The BacLight kit would also allow accurate enumeration of cells. Cells with intact membranes (live) will be stained by the cell permeable SYTO9, while compromised (dead) will stain with the impermeable propidium iodide. It will also allow the identification intermediate populations of cells with slightly compromised membrane, which may then have the potential to repair and replicate should favourable conditions be restored. These will also be characterised by WGS. All applicants must meet the academic entry requirements: https://www.qub.ac.uk/courses/postgraduate-research/biological-sciences-phd.html#entry Research Information PhD Supervisors Information on the research interests and activities of academics in Biological Sciences can be accessed via the School website and the Find a Supervisor facility. Career Prospects Introduction Queen’s postgraduates reap exceptional benefits. Unique initiatives, such as the DegreePlus/Future Ready Award, bolster our commitment to employability, while innovative leadership and executive programmes alongside sterling integration with business experts helps our students gain key leadership positions both nationally and internationally. Career prospects in the biological sciences are exceptionally good. To some extent it depends on the specific topic, of course, but laboratory-based and especially quantitative skills and the proven innovation of a PhD or MPhil are highly sought after. Degrees are very much in demand, both in commercial science and public sector research and development (e.g. drug discovery and development, crop and animal improvements and welfare, sustainable agriculture and resource use, human nutrition and health, animal health, ecological management, food safety and technology, scientific communications, regulation, and many more fields). Employment after the Course Graduates have gone on to be professional research scientists, consultants, or hold technical and junior executive positions in commerce and government. ENTRANCE REQUIREMENTS Graduate The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree in a relevant subject from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School. International Students For information on international qualification equivalents, please check the specific information for your country. English Language Requirements Evidence of an IELTS* score of 6.5, with not less than 5.5 in any component, or an equivalent qualification acceptable to the University is required (*taken within the last 2 years). International students wishing to apply to Queen’s University Belfast (and for whom English is not their first language), must be able to demonstrate their proficiency in English in order to benefit fully from their course of study or research. Non-EEA nationals must also satisfy UK Visas and Immigration (UKVI) immigration requirements for English language for visa purposes. For more information on English Language requirements for EEA and non-EEA nationals see: www.qub.ac.uk/EnglishLanguageReqs. If you need to improve your English language skills before you enter this degree programme, INTO Queen’s University Belfast offers a range of English language courses. These intensive and flexible courses are designed to improve your English ability for admission to this degree. HOW TO APPLY Apply using our online Postgraduate Applications Portal and follow the step-by-step instructions on how to apply. Find a supervisor If you’re interested in a particular project, we suggest you contact the relevant academic before you apply, to introduce yourself and ask questions. To find a potential supervisor aligned with your area of interest, or if you are unsure of who to contact, look through the staff profiles linked here. You might be asked to provide a short outline of your proposal to help us identify potential supervisors.

OVERVIEW Agri-food is the largest indigenous industry on the island of Ireland. With its long coastline of 3,171 km, the island has access to a vast marine environment supporting a vibrant seafood sector as one of the main pillars of the agri-food industry. According to reports the seafood sector contributed € 1.15 billion towards GDP and provided 14,000 jobs. A growing element within the seafood sector is aquaculture, which in 2017 showed a 24% increase in market value. The significance of this industry underlines the fact that sustained production of safe seafood is therefore paramount. Proactive steps are needed to ensure that our seafood is microbiologically safe to prevent any food poisoning outbreaks which could be potentially hazardous to consumer health and financially catastrophic for the sector. This is particularly important since some seafood like oysters are consumed uncooked. Production of safe seafood depends on the microbiological quality of the raw seafood that is harvested from the sea. Vibrio species are a group of bacteria that are indigenous to seawater/seafood and could be pathogenic to both humans and aquatic animals. Human pathogenic species can cause severe food poisoning. Shellfish pathogenic Vibrio can cause economic losses within the aquaculture industry. More importantly, the prevalence of the bacterium in seawater is correlated with warmer temperatures associated with climate change. A systematic survey of Vibrio species in Irish waters has never been conducted. This project will utilize both conventional and molecular approaches to undertake a survey on the prevalence of Vibrio species in seawater/seafood samples obtained off the Irish coast. The surveillance data will help identify the risk factors that support the blooming of Vibrio species in the marine environment. In addition, the data will be used to develop a mathematical model that the fish farmers, fishermen and regulatory bodies can use to predict the prevalence of pathogenic Vibrio species in seawaters. All applicants must meet the academic entry requirements: https://www.qub.ac.uk/courses/postgraduate-research/biological-sciences-phd.html#entry Research Information PhD Supervisors Information on the research interests and activities of academics in Biological Sciences can be accessed via the School website and the Find a Supervisor facility. Career Prospects Introduction Queen’s postgraduates reap exceptional benefits. Unique initiatives, such as the DegreePlus/Future Ready Award, bolster our commitment to employability, while innovative leadership and executive programmes alongside sterling integration with business experts helps our students gain key leadership positions both nationally and internationally. Career prospects in the biological sciences are exceptionally good. To some extent it depends on the specific topic, of course, but laboratory-based and especially quantitative skills and the proven innovation of a PhD or MPhil are highly sought after. Degrees are very much in demand, both in commercial science and public sector research and development (e.g. drug discovery and development, crop and animal improvements and welfare, sustainable agriculture and resource use, human nutrition and health, animal health, ecological management, food safety and technology, scientific communications, regulation, and many more fields). Employment after the Course Graduates have gone on to be professional research scientists, consultants, or hold technical and junior executive positions in commerce and government. ENTRANCE REQUIREMENTS Graduate The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree in a relevant subject from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School. International Students For information on international qualification equivalents, please check the specific information for your country. English Language Requirements Evidence of an IELTS* score of 6.5, with not less than 5.5 in any component, or an equivalent qualification acceptable to the University is required (*taken within the last 2 years). International students wishing to apply to Queen’s University Belfast (and for whom English is not their first language), must be able to demonstrate their proficiency in English in order to benefit fully from their course of study or research. Non-EEA nationals must also satisfy UK Visas and Immigration (UKVI) immigration requirements for English language for visa purposes. For more information on English Language requirements for EEA and non-EEA nationals see: www.qub.ac.uk/EnglishLanguageReqs. If you need to improve your English language skills before you enter this degree programme, INTO Queen’s University Belfast offers a range of English language courses. These intensive and flexible courses are designed to improve your English ability for admission to this degree. HOW TO APPLY Apply using our online Postgraduate Applications Portal and follow the step-by-step instructions on how to apply. Find a supervisor If you’re interested in a particular project, we suggest you contact the relevant academic before you apply, to introduce yourself and ask questions. To find a potential supervisor aligned with your area of interest, or if you are unsure of who to contact, look through the staff profiles linked here. You might be asked to provide a short outline of your proposal to help us identify potential supervisors.

OVERVIEW Recent research suggests that Clostridium difficile is an emerging foodborne pathogen of public health concern and commercial significance for the Irish agri-food sector. This project will initially undertake a systematic literature review to identify gaps in knowledge. Key knowledge deficits to be addressed will include a microbiological survey of cattle, sheep, poultry and pigs on the farm, in the abattoir and on associated meat products. Ready-to-eat (RTE) salads will also be investigated as a vehicle of transmission. All isolates will be subject to initial molecular characterization [ribotyping and PCR testing for the main virulence factors (toxin genes tcdA, tcdB, the binary toxin genes cdtA and cdtB and the tcdR and tcdC regulatory genes)] and antibiotic susceptibility testing. Spore germination and growth in relevant food products/storage conditions (as identified by the gap analysis) will also be investigated. Whole genome sequencing will be used to investigate the genetic relatedness of human clinical isolates and foodborne C. difficile and the virulence potential in a broad range of Irish C. difficile isolates including an assessment of the emergence of new pathogenic strains in the future. A microbiome analysis will be performed in the different ecological niches in which this organism is found. All of the data generated will be used to rank meats and other relevant foods in terms of C. difficile risk, quantitatively assess the effect of season, cross-contamination and cold-chain conditions on the germination efficiency/survival of C. difficile spores and assess the contribution of contaminated meat/other foods to the increased risk of infection in patients treated with antibiotics. All applicants must meet the academic entry requirements: https://www.qub.ac.uk/courses/postgraduate-research/biological-sciences-phd.html#entry Research Information PhD Supervisors Information on the research interests and activities of academics in Biological Sciences can be accessed via the School website and the Find a Supervisor facility. Career Prospects Introduction Queen’s postgraduates reap exceptional benefits. Unique initiatives, such as the DegreePlus/Future Ready Award, bolster our commitment to employability, while innovative leadership and executive programmes alongside sterling integration with business experts helps our students gain key leadership positions both nationally and internationally. Career prospects in the biological sciences are exceptionally good. To some extent it depends on the specific topic, of course, but laboratory-based and especially quantitative skills and the proven innovation of a PhD or MPhil are highly sought after. Degrees are very much in demand, both in commercial science and public sector research and development (e.g. drug discovery and development, crop and animal improvements and welfare, sustainable agriculture and resource use, human nutrition and health, animal health, ecological management, food safety and technology, scientific communications, regulation, and many more fields). Employment after the Course Graduates have gone on to be professional research scientists, consultants, or hold technical and junior executive positions in commerce and government. ENTRANCE REQUIREMENTS Graduate The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree in a relevant subject from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School. International Students For information on international qualification equivalents, please check the specific information for your country. English Language Requirements Evidence of an IELTS* score of 6.5, with not less than 5.5 in any component, or an equivalent qualification acceptable to the University is required (*taken within the last 2 years). International students wishing to apply to Queen’s University Belfast (and for whom English is not their first language), must be able to demonstrate their proficiency in English in order to benefit fully from their course of study or research. Non-EEA nationals must also satisfy UK Visas and Immigration (UKVI) immigration requirements for English language for visa purposes. For more information on English Language requirements for EEA and non-EEA nationals see: www.qub.ac.uk/EnglishLanguageReqs. If you need to improve your English language skills before you enter this degree programme, INTO Queen’s University Belfast offers a range of English language courses. These intensive and flexible courses are designed to improve your English ability for admission to this degree. HOW TO APPLY Apply using our online Postgraduate Applications Portal and follow the step-by-step instructions on how to apply. Find a supervisor If you’re interested in a particular project, we suggest you contact the relevant academic before you apply, to introduce yourself and ask questions. To find a potential supervisor aligned with your area of interest, or if you are unsure of who to contact, look through the staff profiles linked here. You might be asked to provide a short outline of your proposal to help us identify potential supervisors.

OVERVIEW Escherichia coli is a genus of bacteria, encountered as an inhabitant of the human and animal gastrointestinal tract. Surveillance is reporting an increase in resistance to all major classes of antimicrobial agent used in the treatment of livestock and companion animals. An important factor contributing to this increase is the selective pressure imposed by the use/overuse of these valuable therapeutic compounds. Use of antimicrobial compounds in livestock production worldwide is estimated to be approximately double the amount used in human medicine. It is impossible to contain bacteria commensal, pathogenic or otherwise, within the boundary of their original source, whether in the health-care setting or a food-animal production system, which means there is a continuous exchange between bacteria in different niches. Drug-resistant E. coli are recognized as an important reservoir of antibiotic resistant determinants, being disseminated to bacteria of human and veterinary importance. In particular, increasing numbers of reports are describing ESbL-producing bacteria in animals and foods of animal origin. The emergence of resistance to critically important classes of antimicrobial compounds, such as extended spectrum b-lactams (ESbL) is of particular concern. Bacteria expressing an ESbL-resistance phenotype contain plasmids, with the corresponding genetic determinants. This phenotype is associated with a b-lactamase-encoding enzyme of either the TEM; SHV or the more recently described CTX-M families. ESbLs hydrolyse penicillins, lower-generation cephalosporins in addition to 3rd- and 4th-generation cephalosporins. These enzymes are inhibited by clavulanic acid, a feature that is used in their classification. Following geneotype analysis to identify the ESbL-determinant, and using bioinformatic tools, comparisons have identified loci within the plasmids which appear to be conserved. As an example, one of these contains a blaCTX-M-1 gene, located on an IncI1 plasmid. The latter is conserved across several food-producing animal species. Interestingly, no evidence of a blaCTX-M-15 marker has been observed. This research proposal will apply the conventional and molecular microbiological methods developed by the collaborators, to characterise antibiotic resistant E. coli cultured from the three foods of animal origin. All applicants must meet the academic entry requirements: https://www.qub.ac.uk/courses/postgraduate-research/biological-sciences-phd.html#entry Research Information PhD Supervisors Information on the research interests and activities of academics in Biological Sciences can be accessed via the School website and the Find a Supervisor facility. Career Prospects Introduction Queen’s postgraduates reap exceptional benefits. Unique initiatives, such as the DegreePlus/Future Ready Award, bolster our commitment to employability, while innovative leadership and executive programmes alongside sterling integration with business experts helps our students gain key leadership positions both nationally and internationally. Career prospects in the biological sciences are exceptionally good. To some extent it depends on the specific topic, of course, but laboratory-based and especially quantitative skills and the proven innovation of a PhD or MPhil are highly sought after. Degrees are very much in demand, both in commercial science and public sector research and development (e.g. drug discovery and development, crop and animal improvements and welfare, sustainable agriculture and resource use, human nutrition and health, animal health, ecological management, food safety and technology, scientific communications, regulation, and many more fields). Employment after the Course Graduates have gone on to be professional research scientists, consultants, or hold technical and junior executive positions in commerce and government. ENTRANCE REQUIREMENTS Graduate The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree in a relevant subject from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School. International Students For information on international qualification equivalents, please check the specific information for your country. English Language Requirements Evidence of an IELTS* score of 6.5, with not less than 5.5 in any component, or an equivalent qualification acceptable to the University is required (*taken within the last 2 years). International students wishing to apply to Queen’s University Belfast (and for whom English is not their first language), must be able to demonstrate their proficiency in English in order to benefit fully from their course of study or research. Non-EEA nationals must also satisfy UK Visas and Immigration (UKVI) immigration requirements for English language for visa purposes. For more information on English Language requirements for EEA and non-EEA nationals see: www.qub.ac.uk/EnglishLanguageReqs. If you need to improve your English language skills before you enter this degree programme, INTO Queen’s University Belfast offers a range of English language courses. These intensive and flexible courses are designed to improve your English ability for admission to this degree. HOW TO APPLY Apply using our online Postgraduate Applications Portal and follow the step-by-step instructions on how to apply. Find a supervisor If you’re interested in a particular project, we suggest you contact the relevant academic before you apply, to introduce yourself and ask questions. To find a potential supervisor aligned with your area of interest, or if you are unsure of who to contact, look through the staff profiles linked here. You might be asked to provide a short outline of your proposal to help us identify potential supervisors.

OVERVIEW Klebsiella pneumoniae is an opportunistic pathogenic bacterium found in several niches, being often encountered in a biofilm. Infections in at risk populations can result in substantial morbidity and mortality. A mortality rate of around 50% is not uncommon, even with chemotherapeutic intervention. The latter feature may in part be accounted for by the fact that in a biofilm bacterial metabolism slows. When subjected to sub-inhibitory stresses, K. pneumoniae will respond and evolve. Mutations can include single nucleotide polymorphisms (SNPs), as well as the acquisition of mobile genetic elements (MGE), and these can provide a genetic history that can be exploited for therapeutic purposes. Characterisation of these genes/biomarkers by whole genome sequencing (WGS) offers the prospect of developing precision diagnostic tools that may benefit public health by reducing the risk of therapeutic failure. Evolutionary studies have rarely been applied to biofilm models due to a lack of validated methods that simulate the adaption in response to stressors in vivo. This project will – i) develop an in vitro glass bead-based model to study genome scale changes in K. pneumoniae underpinning evolution and adaptation during biofilm development over time in both the presence/absence of sub-inhibitory chemical stressors (including antibacterial agents, biocides and salinity gradients) – ii) characterisation of the observed phenotypes – iii) describe the bacterial transcriptome using RNA-seq – iv) validate a subset of biomarkers using nanopore capture of probe guided DNA duplexes containing SNPs with simultaneous quantification of the mutated bacterial population. Findings can be translated to provide for near-patient testing in clinical real-time via precision diagnostic tools. This project will be supervised by Professor Seamus Fanning of Queen’s University School of Biological Sciences/Institute for Global Food Security and Professor Brendan Gilmore of Queen’s University School of Pharmacy/Institute for Global Food Security. Specific skills/experience required by applicants: Any prospective student would need to have a good background in microbiology (or other related discipline) along with some molecular biology laboratory skills, including whole genome sequencing and basic bioinformatics. All applicants must meet the academic entry requirements: https://www.qub.ac.uk/courses/postgraduate-research/biological-sciences-phd.html#entry Research Information PhD Supervisors Information on the research interests and activities of academics in Biological Sciences can be accessed via the School website and the Find a Supervisor facility. Career Prospects Introduction Queen’s postgraduates reap exceptional benefits. Unique initiatives, such as the DegreePlus/Future Ready Award, bolster our commitment to employability, while innovative leadership and executive programmes alongside sterling integration with business experts helps our students gain key leadership positions both nationally and internationally. Career prospects in the biological sciences are exceptionally good. To some extent it depends on the specific topic, of course, but laboratory-based and especially quantitative skills and the proven innovation of a PhD or MPhil are highly sought after. Degrees are very much in demand, both in commercial science and public sector research and development (e.g. drug discovery and development, crop and animal improvements and welfare, sustainable agriculture and resource use, human nutrition and health, animal health, ecological management, food safety and technology, scientific communications, regulation, and many more fields). Employment after the Course Graduates have gone on to be professional research scientists, consultants, or hold technical and junior executive positions in commerce and government. ENTRANCE REQUIREMENTS Graduate The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree in a relevant subject from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School. International Students For information on international qualification equivalents, please check the specific information for your country. English Language Requirements Evidence of an IELTS* score of 6.5, with not less than 5.5 in any component, or an equivalent qualification acceptable to the University is required (*taken within the last 2 years). International students wishing to apply to Queen’s University Belfast (and for whom English is not their first language), must be able to demonstrate their proficiency in English in order to benefit fully from their course of study or research. Non-EEA nationals must also satisfy UK Visas and Immigration (UKVI) immigration requirements for English language for visa purposes. For more information on English Language requirements for EEA and non-EEA nationals see: www.qub.ac.uk/EnglishLanguageReqs. If you need to improve your English language skills before you enter this degree programme, INTO Queen’s University Belfast offers a range of English language courses. These intensive and flexible courses are designed to improve your English ability for admission to this degree. HOW TO APPLY Apply using our online Postgraduate Applications Portal and follow the step-by-step instructions on how to apply. Find a supervisor If you’re interested in a particular project, we suggest you contact the relevant academic before you apply, to introduce yourself and ask questions. To find a potential supervisor aligned with your area of interest, or if you are unsure of who to contact, look through the staff profiles linked here. You might be asked to provide a short outline of your proposal to help us identify potential supervisors.