Dynamic interplay of protein interactions and modifications – dissection of NLRP3 inflammasome system
Applications are now CLOSED
Protein complexes and protein-protein interaction (PPI) networks are essential mediators of most biological functions. Complexes supporting transient functions such as signal transduction are frequently subject to dynamic remodelling and may depend on post translational modifications (PTMs) as triggers. We and others have shown in previous work that correlative relationships between PPI re-organization and PTMs can be established using quantitative mass spectrometry based analysis of affinity purified target proteins from cells suitably activated in time course experiments with fine temporal resolution( 1,2). In this project we aim to study this relationship and its functional consequences in the NLRP3 inflammasome system—a key hub in innate immune signalling and inflammatory processes with roles in many disease states.
The NLRP3 inflammasome is a multimeric protein complex that acts as an immunological sensor detecting a wide range of microbial- and host-derived signals and, in its active form, promotes cytokine release and inflammatory cell death (pyroptosis). The priming and activation of the NLRP3 inflammasome has been reported to depend on the assembly of various PPIs and on the addition of various PTMs, however, the dynamics and interdependence of these processes have not been systematically evaluated (3,4). We will determine the dynamics of PPI and PTM modulation with respect to the temporal activation state of this system and establish functional relationships to the phenotypic outcomes. Specifically, we aim to: 1) Measure the dynamics of (i) protein complex assembly/disassembly, and (ii) post translational modifications, with fine temporal resolution underlying the priming and activation of the NLRP3 inflammasome with various perturbations; 2) Establish correlative relationships between PPI and PTM dynamics that are indicative of functional relationships; 3) Characterize the molecular and phenotypic consequences of perturbing/removing various components of the system prioritized in aims 1 and 2. We will perform quantitative mass spectrometry-based proteomics analysis of affinity purified target proteins including NLRP3 and the scaffold protein ASC. The NLRP3 inflammasome will be activated in myeloid cells in a time course with fine sampling resolution using a panel of established perturbations such as priming with lipopolysaccharide and TNF and activation with nigericin and R837; and characterized using standard phenotypic assays including ELISAs for IL-1b and IL-18.
LDH release assays and Western blotting for caspase-1 and Gasdermin-D cleavage. We will use data independent acquisition (DIA) mass spectrometry to quantify the PPIs and PTMs. We have previously established the benefits (such as quantitative completeness and linear dynamic range) of this method for measuring dynamic changes in PPIs and PTMs1. Specifically we will use the diaPASEF method that we have recently co-developed as it substantially reduces the amount of starting material required facilitating the analysis of large numbers of timepoints/perturbations(5). The output will be a quantitative picture of PPI and PTM modulation in the NLRP3 inflammasome system that will be subjected to correlative analysis to establish relationships between PPIs and PTMs in this system. The most promising targets of this analysis will be prioritized for functional characterization using CRISPR-Cas9 deletion or point mutation in an induced pluripotent stem cell (iPSC)-derived macrophage model using phenotypic assays including measurement of ASC speck formation, cytokine release (ELISA), cell death (LDH) and cleavage of key substrates (Western blot). The expected outcomes of the study will be (i) insight into the interdependence of PPIs and PTMs in dynamic signalling systems, and, (ii) a systematic evaluation of the molecular changes, and their functional consequences, in the activation of the NLRP3 inflammasome. These insights will inform our understanding of the fundamental biology of this key inflammatory signalling pathway and may also identify new targets for the development of anti-inflammatory therapies.
The successful candidate will join the Collins and Coll research teams at QUB benefitting from state-of-the-art technology and training in quantitative mass spectrometry, computational biology, biochemistry, immunology and cell biology as well as support to develop essential research skills, project management, scientific writing and communication.
2.1 degree or higher essential, MSc/MSci desirable. Experience in mass spectrometry-based proteomics, tissue culture, general molecular biology, protein purification, computational biology desirable but not essential.
How to apply:
All applications must be submitted via the Queen's Direct Applications Portal: https://dap.qub.ac.uk/portal/user/u_login.php
1. Collins, B. C. et al. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat. Methods 10, 1246–1253 (2013) https://doi.org/10.1038/nmeth.2703
2. Zheng, Y. et al. Temporal regulation of EGF signalling networks by the scaffold protein Shc1. Nature 499, 166–171 (2013) https://doi.org/10.1038/nature12308
3. McKee, C. M. & Coll, R. C. NLRP3 inflammasome priming: A riddle wrapped in a mystery inside an enigma. J. Leukoc. Biol. 108, 937–952 (2020) https://doi.org/10.1002/JLB.3MR0720-513R
4. Swanson, K. V., Deng, M. & Ting, J. P.-Y. The NLRP3 inflammasome: molecular activation and regulation to therapeutics. Nat. Rev. Immunol. 19, 477–489 (2019) https://doi.org/10.1038/s41577-019-0165-0
5. Meier, F. et al. diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition. Nat. Methods 17, 1229–1236 (2020) https://doi.org/10.1038/s41592-020-00998-0
Applicants for this project will be in competition for a studentship funded by the Department for the Economy (DfE). Candidates must meet UK residency and citizenship criteria in order to be considered eligible.
Dr Ben Collins
Full-time: 3 years
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.
There are three broad themes to research at the School:
- Agri-Food Systems and Human Nutrition
- Understanding Health and Disease
- Sustaining Ecosystems and Biodiversity
Agri-Food Systems and Human Nutrition:
This theme focuses on how Agri-Food systems can be better positioned to provide safe and healthy diets and high quality of animal products and support human and animal health in a way that is environmentally sustainable and resilient to climate change.
Underpinning these goals, the disciplinary expertise of the theme integrates basic and applied research from animal health and welfare, nutrition, performance and environmental impact (e.g. greenhouse gas emissions from livestock) to chemical contaminant detection, food microbiology, fraud detection and food systems traceability and transparency.
Supported by underpinning technological expertise in cutting edge molecular, genomic, transcriptomic/proteomic and metabolomic methods, the goal of the theme is to transform Agri-Food systems so that they benefit both human nutrition and health while simultaneously reducing the greenhouse gases emissions from livestock production systems, protecting ecological resources, supporting livelihoods and affordable foods, and upholding social, cultural, and ethical values.
Understanding Health and Disease:
The Understanding Health and Disease research theme covers humans, plants, and animals with research strengths in prevention, diagnostics, surveillance, epidemiology, and treatments. We study how health can be improved through food and nutrition and how diseases can be tackled by understanding their fundamental molecular mechanisms, including those underpinning the biology of pathogens and parasites. Our researchers work in human cancer and genetic diseases, in infections caused by bacteria, fungi, viruses, and parasites, and in how global health and disease will be affected by global warming and climate change.
We recognize that the only way to tackle the problems we face as a society is to take an interdisciplinary approach to our research. This means we have expertise in broad areas including molecular biology, biochemistry, bioinformatics, genomics, transcriptomics, modelling, bioanalytical chemistry, proteomics, metabolomics, microbiology, parasitology, and plant biology. We work internationally with researchers and partners in universities, charities, non-governmental organisations, industry, and government agencies to tackle local and global challenges.
Sustaining Ecosystems and Biodiversity:
This theme covers research in 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, environmental microbiology, microbial ecology, food web analysis, microcosm and mesocosm experiments, and mathematical/computational methods. Within this theme we also 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 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.
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
- Research at Institute for Global Food Security and the School of Biological Sciences was rated 1st in the UK in the latest Research Exercise Framework (REF) – an independent assessment of research quality, impact and environment at UK universities.
IGFS/Biological Sciences topped the national league table for Agriculture, Veterinary and Food Science, with 94% of research in those areas deemed “world-leading” or “internationally excellent”.
Additionally, the research environment at IGFS/SBS scored a phenomenal 100%.
- Most of the critical problems facing humanity - disease, climate change and food security - require biological understanding to solve them.
My collaborative PhD with the Institute for Global Food Security and the Agri-Food and Biosciences Institute has given me opportunities to teach, attend seminars and conferences, and to develop a range of skills. I have enjoyed my PhD and my supervisors and funding body (DAERA) have been welcoming, supportive and encouraging of my research.
Dr Rebekah McMurray, Biological Sciences PhD
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.
Learning OutcomesA 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.
Course structureResearch 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 desk in a shared office space.
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||£4,596|
|Republic of Ireland (ROI) 2||£4,596|
|England, Scotland or Wales (GB) 1||£4,596|
|EU Other 3||£23,850|
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. 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.
More information on postgraduate tuition fees.
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.
Some research programmes incur an additional annual charge on top of the tuition fees, often referred to as a bench fee. Bench fees are charged when a programme (or a specific project) incurs extra costs such as those involved with specialist laboratory or field work. If you are required to pay bench fees they will be detailed on your offer letter. If you have any questions about Bench Fees these should be raised with your School at the application stage. Please note that, if you are being funded you will need to ensure your sponsor is aware of and has agreed to fund these additional costs before accepting your place.
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.
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Apply using our online Postgraduate Applications Portal and follow the step-by-step instructions on how to apply.
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