Bovine TB: Reconstructing the molecular evolution of Mycobacterium bovis
Applications are now CLOSED
Bovine tuberculosis (TB) is an infectious mycobacterial disease caused by Mycobacterium tuberculosis var. bovis, a pathogenic member of the M. tuberculosis complex bacteria. It is the most costly, problematic and controversial endemic zoonosis currently facing government, the farming industry and veterinarians in the UK and Ireland with annual control costs estimated currently at £40M for N Ireland and €84M for Ireland. The epidemiology of bovine TB is notoriously complex and still lacking in detail, with current evidence indicating both cattle and wildlife sources. Additional information that would guide the use of control management strategies on a more science- and evidence-based footing would be of great value to policy-makers and stakeholders.
DAFM (Ireland) and DAERA (N Ireland) have co-funded the UCD-led project: BTBGENIE (Bovine TuBerculosis GENomics IrEland): The project, which focuses on the development of genomic epidemiology systems for tracking and eradicating Mycobacterium bovis in Ireland will benefit from recent advances in genomics methodologies and parallel bioinformatics pipelines. Whole-genome sequencing (WGS) now provides a step-change in our ability to characterize pathogens. BTBGENIE aims to integrate pathogen WGS more fully into the TB control programmes and to investigate the transmission, epidemiology and evolution of M. bovis in Ireland. This PhD project is integral to the BTBGENIE project. The student will have access to an unprecedented bio-bank of M. bovis isolates, collected on the island of Ireland over years and from various hosts and ~1,000 M. bovis whole-genome sequences.
Available infrastructure resources:
The student will have in-house access to both genome NGS sequencing platforms (Illumina MiSeq, HiSeq and NovaSeq) and dedicated High Performance Computer infrastructure in AFBI, QUB and UCD. Professor Prodohl’s laboratory in QUB also provides direct access to state of the art medium- high- throughput automated SNP genotyping technology that will be used to screen multiple bacterial isolates for clade-defining markers identified by WGS, thereby permitting high-resolution phylogeographic analyses of M. bovis diversity.
General PhD objectives are:
1) To construct a phylogeny for M. bovis in Ireland for comparison with other areas in Britain and elsewhere.
2) To investigate potential signatures of selection within identified evolutionary lineages.
3) To identify and map M. bovis genetic structure and diversity in Ireland; investigating phylogeographic distribution of sequence / strain types and their wider dispersal.
4) Use genomic data, to detect and estimate the relative importance of bi-directional, cross border dissemination of bovine TB in Ireland.
The student will be trained in collection and management of large genomics datasets, state of the art phylogenetic comparative approaches in R and mathematical models of evolution (including detecting potential signatures of genomic selection), and will capitalise on the availability of Queen’s University High Performance Computing resources (KELVIN). The student will also have the opportunity to interact with researchers of the wider BTBGENIE team at QUB, AFBI and UCD.
In addition to addressing discovery and translational research questions on a topic of national and international significance, the student will gain a valuable set of interdisciplinary skills that increase employability, including cutting-edge statistical and mathematical modelling, data management, numeracy, evaluating risk and uncertainty, as well as gaining an in-depth understanding of fundamental principles in microbial evolution, pathogen genomics and epidemiology. Through interactions with AFBI researchers,the student will also gain a better understanding of disease surveillance and management and some of the skills required to inform policy.
This project will be supervised by Professor Paulo Prodohl and Dr Rosaleen Hynes (QUB) and Dr Adrian Allen and Professor Robin Skuce (AFBI). The project advisor is Professor Stephen Gordon of UCD.
Brites D, Loiseau C, Menardo F, et al. A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex. Front Microbiol. 2018;9:2820. Published 2018 Nov 27. doi:10.3389/fmicb.2018.02820
Chiner-Oms Á, Sánchez-Busó L, Corander J, et al. Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex. Sci Adv. 2019;5(6):eaaw3307. Published 2019 Jun 12. doi:10.1126/sciadv.aaw3307
Crispell J, Benton CH, Balaz D, et al. Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system. Elife. 2019;8:e45833. Published 2019 Dec 17. doi:10.7554/eLife.45833
Smith NH, Gordon SV, de la Rua-Domenech R, Clifton-Hadley RS, Hewinson RG. Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nat Rev Microbiol. 2006;4(9):670–681. doi:10.1038/nrmicro1472
Candidates should have (or expect to achieve) a minimum of a 2.1 Honours degree in a relevant subject (e.g. Biological subject or Computer Sciences). Applicants with a minimum of a 2.2 Honours degree may be considered providing they have a Distinction at Master’s level.
This project is funded by a DAFM/DAERA Partnership to support collaborative research in agreed priority areas across both jurisdictions. The studentship provides funding for tuition fees, stipend and research training and support grant subject to eligibility.
Please note that the studentship will cover a maximum of €6,000 per annum of the QUB tuition fees for non-EEA students. Non-EEA students may also be required to apply for a visa in order to travel from the UK to the Republic of Ireland.
Biological Sciences overview
The School of Biological Sciences provides PhD and MPhil (research degree) programmes in subjects ranging from basic biochemistry, molecular genetics and cancer research, to agricultural science, marine ecology and the economic evaluation of ecosystem services and food retailing. If you have a topic or research question in mind, please use the Find a Supervisor link (see Apply tab) to identify the most appropriate member of staff to support your idea. If not, don't worry, we regularly advertise funded projects and there is no harm in browsing our academic staff profiles for inspiration and then contacting whoever seems best: we are very open to applications from suitably qualified people interested in scientific research. In every case, a PhD or MPhil course provides the means of being part of a cutting edge scientific research team and contributing to genuine new discoveries or the development of new methods for practical use. If you cannot study full time, we offer pro-rata part time research degree programmes as well.
To help orientation, the School is organised into three research theme clusters:
- Ecosystem Biology and Sustainability
- Microbes and Pathogen Biology
- Food Safety and Nutrition
Ecosystem Biology and Sustainability:
In this cluster, you could research biodiversity and ecosystem services for environments ranging from tropical forests to deep oceans, using field techniques and skills such as wildlife tracking, taxonomy, geostatistics, molecular and genetic ecology, foodweb-analysis, microcosm and mesocosm experiments and mathematical/computational methods. Alternatively, you could study the behaviour and temperament of wild, agricultural or domestic animals and their implications for welfare and ability to respond to environmental change. Potential research projects include phylogenetic analysis of rare and newly discovered species, examination of ecological interactions in tropical systems, agricultural soils, or marine communities, using state-of-the-art genetic analysis, surveys using drones or satellite tagging, or experiments in tanks and field plots, including careful and ethical examinations of animal behaviour. Projects range from theoretical analysis of stability in ecosystems, through discovery of new species and mechanisms of interaction, or responses to climate change, to the assessment of EU agri-environment schemes, development of new methods for commercial fisheries management and economic evaluations of conservation measures. Projects very often have an international dimension and include collaboration with other researchers worldwide.
Microbes and Pathogen Biology:
This cluster covers a diverse array of research interests united by an emphasis on molecular approaches applied to both fundamental and applied questions over the range from molecular to ecological systems. These interests include biochemistry, food safety, microbiology and parasite control with applications in human and animal health, nutrition, plant and soil sciences, and agricultural development. We have a long-standing reputation in parasite biology and in applied microbiology (for example in clearing land of contamination) as well as strong contributions to fundamental methods in understanding cancer, developing veterinary vaccines and molecular detectors for toxins and diseases. The common thread is our strong molecular approach using and developing cutting edge genomic, transcriptomic/proteomic methods. Research students in this cluster enjoy a range of strong international links across Europe, Asia, North and South America.
Food Safety and Nutrition:
Research opportunities offered by this cluster span the entire food chain "from farm to fork" with a strong emphasis on food safety and nutrition, public health and food security. In this cluster you would conduct research under the supervision of leading scientists based in the Institute for Global Food Security and benefit from integration with business experts, helping you gain leadership positions nationally and internationally.
Biological Sciences Highlights
- The School has a wide range of strong, international links with governments, academia and industry, into which postgraduate research students are integrated.
World Class Facilities
- Research students will have access to laboratory space as required (in our state-of-the-art research laboratories) and where relevant, also a range of field study sites and equipment (e.g. remote sensing drone equipment). They also have access to local and campus-wide high performance computing facilities and the full strength of our world-class library. Many students also benefit from the strong collaboration network maintained by our academic staff, which could result in working in the laboratories of partner organisations in industry and government as well as in the University, under specific arrangements.
- Students studying in the Food Safety and Nutrition programme will gain excellent practical experience of advanced technology and bioanalytical techniques for food safety analysis and monitoring, including:
1. GC, HPLC and UPLC separation platforms;
2. ICP, IR, qToF and QqQ mass spectrometers;
3. Microbiological research facilities;
4. Antibody production and biomolecule binder development;
5. Cell culture suite and bioanalytical assay detection systems;
6. NMR, NIR and Raman spectrometers;
7. Proteomic and metabolomic profiling tools RT-PCR;
8. Transcriptomic profiling;
9. Next-generation sequencing;
10. Multiplex biosensor platforms and LFD development.
Internationally Renowned Experts
- Queen's ranking for Food Science research was first in the UK in the Times and Sunday Times Good University Guide 2021.
In the Complete University Guide 2021, Queen's was joint first in the UK for Research Intensity in Biological Sciences.
- Most of the critical problems facing humanity - disease, climate change and food security - require biological understanding to solve them.
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 (see Apply tab).
Queen's postgraduates reap exceptional benefits. Unique initiatives, such as Degree Plus and Researcher Plus 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.
People teaching you
Dr Gareth Arnott
Postgraduate Research Director
School of Biological Sciences
For a PhD you will have a principal and second supervisor who advise your independent studies and will be supported by a wider team from the academic staff - who they are, of course, depends on your project. For further details on any aspect of postgraduate research degrees within the School of Biological Sciences, contact: email@example.com. Research degrees are overseen by the School of Biological Sciences Director of Postgraduate Research, who currently is Dr Gareth Arnott.
A postgraduate research degree involves the undertaking of independent research under the guidance of a professional academic supervisory team, typically using the laboratory facilities on offer in one or more of the teams' labs. The student will be expected to develop their own ideas and learn the methods needed to test them empirically and theoretically. This usually involves learning and practising both laboratory (and or field) skills as well as developing a strong theoretical background in the relevant subject.
As well as practical work, all the activities of independent academic scholarship, such as literature searching and critical appraisal, written and verbal communications and academic networking will be developed during a research degree. Independence and innovation will be strongly encouraged, but the student will be supported by regular supervisory guidance and a wide range of courses will also be on offer, both in subject specific skills and generic skills, especially supported by the Graduate School (https://www.qub.ac.uk/graduate-school/).
Students are encouraged to interact with one another and with members of academic staff and postdoctoral scientists to build confidence and informal learning, through a range of ‘research culture’ activities, including peer groups where students get together to discuss topical research papers, or methods, or just chat about their interests.
Research degrees vary in length, but typically for a PhD they are three or four years long (full-time) and double that for part-time studies. They follow an annual cycle of progress with formal panel-based appraisals of the progress, the outcome of which is typically practical and academic advice about how to overcome problems encountered and how to move to the next stage. During each year, students are expected to supplement their studies with some tailored courses, ranging from highly specific (e.g. learning to use a piece of apparatus or technique) to generic (e.g. developing oral presentation or leadership skills). Every stage is supported by the supervisory team, augmented by an independent panel of progress monitors as well as the full support of the Graduate School.
Assessment processes for the Research Degree differ from taught degrees. Students will be expected to present drafts of their work at regular intervals to their supervisor who will provide written and oral feedback; a formal assessment process takes place annually.
This Annual Progress Review requires students to present their work in writing and orally to a panel of academics from within the School. Successful completion of this process will allow students to register for the next academic year.
The final assessment of the doctoral degree is both oral and written. Students will submit their thesis to an internal and external examining team who will review the written thesis before inviting the student to orally defend their work at a Viva Voce.
Supervisors will offer feedback on draft work at regular intervals throughout the period of registration on the degree.
Full-time research students will have access to a shared office space and access to a desk with personal computer and internet access.
The minimum academic requirement for admission to a research degree programme is normally an Upper Second Class Honours degree from a UK or ROI HE provider, or an equivalent qualification acceptable to the University. Further information can be obtained by contacting the School.
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.
|Northern Ireland (NI) 1||£TBC|
|Republic of Ireland (ROI) 2||£TBC|
|England, Scotland or Wales (GB) 1||£TBC|
|EU Other 3||£22,700|
1 EU citizens in the EU Settlement Scheme, with settled or pre-settled status, are expected to be charged the NI or GB tuition fee based on where they are ordinarily resident, however this is provisional and subject to the publication of the Northern Ireland Assembly Student Fees Regulations. Students who are ROI nationals resident in GB are expected to be charged the GB fee, however this is provisional and subject to the publication of the Northern Ireland Assembly student fees Regulations.
2 It is expected that EU students who are ROI nationals resident in ROI will be eligible for NI tuition fees, in line with the Common Travel Agreement arrangements. The tuition fee set out above is provisional and subject to the publication of the Northern Ireland Assembly student fees Regulations.
3 EU Other students (excludes Republic of Ireland nationals living in GB, NI or ROI) are charged tuition fees in line with international fees.
All tuition fees quoted are for the academic year 2021-22, and relate to a single year of study unless stated otherwise. Tuition fees will be subject to an annual inflationary increase, unless explicitly stated otherwise.
Biological Sciences costs
Students may incur additional costs for small items of clothing and/or equipment necessary for lab or field work
Additional course costs
Depending on the programme of study, there may also be other extra costs which are not covered by tuition fees, which students will need to consider when planning their studies . Students can borrow books and access online learning resources from any Queen's library. If students wish to purchase recommended texts, rather than borrow them from the University Library, prices per text can range from £30 to £100. Students should also budget between £30 to £100 per year for photocopying, memory sticks and printing charges. Students may wish to consider purchasing an electronic device; costs will vary depending on the specification of the model chosen. There are also additional charges for graduation ceremonies, and library fines. In undertaking a research project students may incur costs associated with transport and/or materials, and there will also be additional costs for printing and binding the thesis. There may also be individually tailored research project expenses and students should consult directly with the School for further information.
How do I fund my study?1.PhD Opportunities
Find PhD opportunities and funded studentships by subject area.2.Funded Doctoral Training Programmes
We offer numerous opportunities for funded doctoral study in a world-class research environment. Our centres and partnerships, aim to seek out and nurture outstanding postgraduate research students, and provide targeted training and skills development.3.PhD loans
The Government offers doctoral loans of up to £26,445 for PhDs and equivalent postgraduate research programmes for English- or Welsh-resident UK and EU students.4.International Scholarships
Information on Postgraduate Research scholarships for international students.
Funding and Scholarships
The Funding & Scholarship Finder helps prospective and current students find funding to help cover costs towards a whole range of study related expenses.
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.