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FOODBIOSYSTEMS - Temperature regulation of microRNAs and crop - rhizosphere interactions

School of Biological Sciences | PHD

Applications are now CLOSED
Funding
Funded
Reference Number
SBIO-2020-1078
Application Deadline
6 March 2020
Start Date
1 October 2020

Overview

* APPLY VIA: https://research.reading.ac.uk/foodbiosystems/apply-for-a-phd/ * * DO NOT APPLY DIRECTLY TO QUEEN'S FOR THIS PHD PROJECT * Plants manipulate the rhizosphere (soil surrounding the plant root) through the release of water-soluble and volatile organic compounds known collectively as root exudate. Root exudate can recruit beneficial soil microflora and fauna; however, it can also attract parasites and pathogens, with implications for plant health and yield. Our preliminary data demonstrate that temperature alters tomato root exudate composition, which affects the hatching and attraction of economically important plant parasites and microbes. Understanding the impact of temperature on important plant-rhizosphere interactions will help to develop climate-smart approaches to crop protection, driving the sustainable intensification of agriculture. We have generated transcriptomic datasets from developmentally-matched tomato seedlings grown independently at 18, 23 and 28 degrees C. Our data indicate that non-coding microRNAs and predicted target genes are differentially expressed as a factor of temperature. MicroRNAs regulate the expression of target genes in a sequence-dependent manner, modulating diverse aspects of plant physiology and function. Individual microRNAs have the potential to regulate hundreds of transcripts simultaneously. On that basis, microRNAs and/or microRNA target sites on targeted genes, represent an attractive focal point for breeding / biotechnology and novel crop improvement strategies. Our data identify a range of target genes that demonstrate asymmetric differential expression relative to their cognate microRNA, belong to a wide range of families, including ATPBinding Cassette (ABC) transporters, Multidrug And Toxic compound Extrusion (MATE) transporters, Ethylene Response Factors (ERFs), UDP-glycosyltransferases, and sugar transporters, which have all been linked to the control of root exudate composition previously. We hypothesise that these microRNAs and target genes contribute to the modification of root exudate composition and altered interactions with parasites and microbes as a factor of temperature.

The goal of this project is to link selected temperature-regulated microRNAs and target genes to specific changes in root exudate composition, and altered plant-rhizosphere interactions. We will address this goal by confirming microRNA-mRNA interactions (transcriptomics and degradome sequencing) and investigating
microRNA and target gene functions (transgenic over-expression / microRNA decoys / RNA interference). We will
then assess parasite / microbe behaviours for a range of organisms, including Globodera pallida, Meloidogyne
incognita, Bacillus subtilis, Pseudomonas aeruginosa, Agrobacterium tumefaciens, Funneliformis and Rhizophagus species (hatching / attraction / invasion / biofilm formation / Vir gene induction / spore
germination / hyphal branching etc. as appropriate to individual species). We will also assess exudate compositional change using metabolomics (LC-Qtof-MS and GC-MS).

A core driver for this proposal is our recently discovered ability to alter the behaviour of selected plant pathogens and microbes within the rhizosphere by manipulating plant root exudate composition using
temperature. This finding provides a new opportunity to: (i) dissect exudate-pathogen interplay to optimise the selection of beneficial (pathogen inhibiting) exudate components; (ii) identify the mechanisms driving beneficial plant root exudate changes. This project will link individual temperature-regulated microRNAs and target genes to specific changes in root exudate chemistry, and altered plant-rhizosphere interactions. These microRNAs and target genes could be exploited for crop improvement through breeding, genome editing or biotechnology. Likewise, an understanding of the exudate compounds that influence organismal behaviour in the rhizosphere would be valuable, and could lead to new methods of rhizosphere engineering.

Training opportunities: Technical training will include: transcriptomics and bioinformatics; core molecular techniques (including DNA / RNA extraction, qRT-PCR etc.); plasmid design and construction; plant transgenesis;
reverse genetics; parasite and microbe behavioural assays / AMF interaction assays will be taught in conjunction with collaborators in the Pelligrino lab (Scuola Superiore Sant’Anna [SSSA; Pisa, Italy]); metabolomics and data analysis; training in communication with the general public, including children through workshops/school visits.

Attendance at diverse national and international conferences will provide further opportunities to develop presentation skills and network with peers. QUB offers a wide range of training courses in conjunction with the Graduate School, and the ‘Postgraduate
Development Programme’. Likewise, The University of Reading offers the ‘Reading Researcher Development Programme’. Collectively, these programmes offer a broad range of relevant skills and training opportunities for the student.

There will also be opportunities to collaborate with international partners in Kenya / Ghana, to explore opportunities to translate project outcomes into the sub-Saharan Africa context.

Student profile: This project would suit a student with a degree in biological science / microbiology / plant biology, who has a keen interest in plant interactions. The successful student should be willing to learn a wide
variety of technical skills and apply a creative mind-set to this challenging project. Previous experience in plant sciences, molecular biology, bioinformatics, nematology, microbiology would be beneficial, but not strictly required.

Funding Information

This project is part of the FoodBioSystems BBSRC Doctoral Training Partnership (DTP), it will be funded subject to a competition to identify the strongest applicants. Due to restrictions on the funding, this studentship is only open to UK students and EU students who have lived in the UK for the past three years. The FoodBioSystems DTP is a collaboration between the University of Reading, Cranfield University, Queen’s University Belfast, Aberystwyth University, Surrey University and Brunel University London. Our vision is to develop the next generation of highly skilled UK Agri-Food bioscientists with expertise spanning the entire food
value chain. We have over 60 Associate and Affiliate partners. To find out more about us and the training programme we offer all our postgraduate researchers please visit
https://research.reading.ac.uk/foodbiosystems/

Project Summary
Supervisor

Dr Johnathan Dalzell


Funding Body
FoodBioSystems BBSRC Doctoral Training Partnership
Apply now Register your interest

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
Industry Links
  • 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
  • Students will have the full use of modern, world-class laboratories, equipped with state-of-the-art, highly advanced analytical instruments and facilitated by world-class field work provision.
  • 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.
Key Facts

  • Over 80% of science jobs are in areas of Biological Sciences.
  • Most of the critical problems facing humanity - disease, climate change and food security - require biological understanding to solve them.
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Course content

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 (see Apply tab).

Career Prospects

Introduction
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.

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 Keith Farnsworth
Chair of School Postgraduate Research Committee
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: biosciences-pg@qub.ac.uk.

Learning Outcomes

A research degree offers students an opportunity to foster their capacity for independent research and critical thought. It also allows students to explore an area of interest and so understand and solve theoretical and practical problems within the field. Undertaking a research degree can enhance a student’s written and oral communication skills and a PhD is almost always a formal requirement for an academic post.

Course structure

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Assessment

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.

Feedback

Supervisors will offer feedback on draft work at regular intervals throughout the period of registration on the degree.

Facilities
Full-time research students will have access to a shared office space and access to a desk with personal computer and internet access.

Entrance requirements

Graduate
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.

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.

  • Academic English: an intensive English language and study skills course for successful university study at degree level
  • Pre-sessional English: a short intensive academic English course for students starting a degree programme at Queen's University Belfast and who need to improve their English.

Tuition Fees

Northern Ireland (NI) £4,407
England, Scotland or Wales (GB) £4,407
Other (non-UK) EU £4,407
International £21,300

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

All Students

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.Doctoral Training Centres at Queen's

Queen's has eight outstanding competitive Doctoral Training Centres, with each one providing funding for a number of PhD positions and most importantly a hub for carrying out world class research in key disciplines.

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, £10,000 for students in Scotland and up to £5,500 for Northern Ireland 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

Apply using our online Postgraduate Applications Portal go.qub.ac.uk/pgapply 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.