Plant Biology projects

Please try to identify a research project that suits you.  This is to ensure a proper match between your research interests and your prospective supervisor. We do not encourage applications to more than one project however we would encourage informal discussions with different project supervisors to help you decide which project to apply to. Contact details for academic staff can be found on each project description.

Mechanisms of palladium uptake and nanoparticle formation in planta. Supervisors: Prof Neil Bruce & Dr Frans Maathuis

Platinum group metals (PGMs) are used in a bewildering variety of industrial applications, often in the form of nanoparticles (NPs). However, as they are dispersed increasingly throughout the environment, the usage of these precious elements is a growing concern. Our studies, in collaboration with the University of York Green Chemistry for Excellence centre, have demonstrated that plants can take up PGMs, producing NPs which can be used to make high-performing plant-based catalysts. Uptake can be from metal waste sources, including mine tailings and subsequent NP extraction is not necessary, presenting a technology with potentially fewer processing steps and green chemical applications, all using an environmentally restorative approach. This project will combine the state-of-the-art technologies of synthetic biology, imaging and genomics to identify genetic mechanisms behind, and enhance the production of, PGM uptake and NP formation in plants. Additionally, the project will link with Green Chemistry, where catalytic properties of NP-containing plant biomass will be tested.

Supervisors: Prof Neil Bruce & Dr Frans Maathuis

To discuss your suitability for this project please email: neil.bruce@york.ac.uk

Please read the 'How to apply' tab before submitting your application.

How to set a circadian clock: structural mechanism of ELF3-ELF4 clock-protein action in transcriptional repression. Supervisors: Prof Seth Davis & Prof Anthony Wilkinson

The circadian clock is required to set metabolism and development to the appropriate time of day. As the rising of the morning sun changes by up to 7 minutes a day, mechanisms exist to reset this clock so that it is in harmony with prevailing conditions, and this process is called entrainment. The mechanism of plant photoreceptor signalling to the circadian oscillator remains unknown. Our previous identification of ELF4 and ELF3 as components of the key complex required for the oscillator to cycle and our genetic finding that this complex is the target of phytochrome photoreceptor entry to this clock sets up a series of programmes to mechanistically resolve an entrainment mechanism and this answers a long-standing question in circadian chronobiology, termed Aschoff's Rule, whereby increases in light intensity lead to periodicity acceleration.

The proposed project starts from a systems-genomic approach i) to define when and where the ELF4 / ELF3 complex target transcriptional repression, ii) moves to examine the roles of timing in said repression and then iii) to describe the role of light perception in modulating their target association. New technical approaches to find chromatin targets facilitate these experiments. From there, molecular-biological approaches would be used to improve the understanding of the structure-function relationship of the ELF4 and ELF3 repression cycle through characterisation of their timed complex assembly n the living plant cell. Novel cellular-imaging and luciferase-imaging approaches will be employed to study the kinetics of these events, and determine photoreceptor occupancy in their complex. Efforts to solve by crystallography the structure of the ELF4 / ELF3 repression complex will be undertaken and, in parallel, associated in vitro biophysics of complex assembly will be elucidated. All of these will be connected back to the molecular-physiological action of oscillator behaviour and the cellular-movement events that coincide with regulated complex formation. Taken together this project is envisaged to provide the mechanistic basis of a long-standing problem and be the first description of a clock-resetting mechanism in plants.

References: Anwer et al. eLife e02206 (2014); Herrero et al. Plant Cell 24: 428–443 (2012); Levdikov et al. Proc. Natl. Acad. Sci. USA 109, 5441-5445 (2012); Kolmos et al. Plant Cell 23: 3230-3246 (2011)

Supervisors: Prof Seth Davies (Biology) & Prof Anthony Wilkinson (Chemistry)

To discuss your suitability for this project please email: seth.davies@york.ac.uk

Please read the 'How to apply' tab before submitting your application.

 

DEZ-dependent pathways of cell wall signalling in photomorphogenesis. Supervisors: Dr Mike Haydon & Prof Simon McQueen-Mason

The plant cell wall is a complex and dynamic structure comprised of a matrix of complex carbohydrate polymers and proteins. Understanding plant cell wall biosynthesis and function has emerged as an important question in plant biology because of the implications for biofuel production. Plant cell walls provide cellular structure and strength, while permitting plasticity of the plant form and thus are a fundamental aspect of plant physiology and development. As the interface to the external environment, cell walls provide a crucial barrier to environmental stress, such as pathogens, drought and wounding. Important questions are emerging about the role of cell walls in sensing the environment and the implications of altered cell wall composition on plant physiology. Thus, cell wall signalling is an emerging field in plant sciences, gaining widespread interest.

A critical stage in plant development is the transition from heterotrophy to photoautotrophy in emerging seedlings and the establishment of photomorphogenesis (light-dependent growth). Much has been learned about light signalling in plants from constitutive photomorphogenic (cop) and deetiolated (det) mutants of Arabidopsis, which develop abnormally as light-grown seedlings when germinated in the dark. We identified a mutant of Arabidopsis called deetiolated by zinc (dez), which is conditionally photomorphogenic in the dark when grown on media containing high concentrations of Zn. DEZ encodes a putative cell wall acetyltransferase and the mutation alters cell wall composition and activates phytochrome-dependent light signalling pathways. Our current model centers on Ca2+ signalling and jasmonic acid (JA) signalling pathways, triggered from the altered cell wall, activating light signalling pathways for photomorphogenesis.

To better understand these pathways, we have used forward genetic screens to identify non-allelic mutants with dez-like phenotypes, as well as extragenic suppressors of dez. This project will directly test our model using state-of-the-art tools to understand the role of Ca2+ and JA signalling in dez, dez-like and suppressor of dez mutants. To determine the physiological impact and evolutionary advantage of the signalling pathway(s) developmental, physiological and molecular phenotypes will be assessed in these mutants. Alterations to cell wall composition, digestibility and cell structure in the mutants will be determined using a range of analytical assays, cell staining and in vivo imaging techniques. Mutations will be mapped by shotgun whole-genome resequencing and the gene products will be functionally characterised to determine their cellular function in DEZ-dependent signalling pathways.

Supervisors: Dr Mike Haydon & Prof Simon McQueen-Mason

To discuss your suitability for this project please email: mike.haydon@york.ac.uk

Please read the 'How to apply' tab before submitting your application.

 

 

Examining climate change impacts on insect pest-crop plant interactions. Supervisors: Prof Jane Hill & Prof Sue Hartley

Project background
Many insect pest are predicted to increase in the UK under future climate warming leading to reduced crop yields and increased pesticide use. Our research has shown that insects are shifting their distributions northwards (i.e. becoming more common in the UK), advancing their phenologies (e.g. developing through more generations per year), and altering the range of larval host plants in their diet (i.e. having the potential to feed on a wider range of crop plants). However, the biochemical basis of these insect-plant interactions are poorly known making impacts of climate change on crop yields and pest incidence hard to predict. Our recent metabolomics studies have revealed how variation in plant secondary compounds varies among a group of plants used by a single herbivore species, the challenge now is to determine how this variation affects insect diet choice, growth and development, and interactions with environmental factors.

Objectives
The project will examine the degree to which insect larval host diet is affected by climate change (temperature and CO2). The project will study Lepidoptera (Silver Y moth Autographa gamma, small white butterfly Pieris rapae) feeding on brassicales species, and focus on examining the consequences of variation in plant secondary metabolites under elevated temperature and CO2 and their impacts on insect growth and survival.

Novelty & Timeliness
Understanding climate change impacts on plant secondary metabolites is poorly understood yet is likely to have a considerably impact on their insect pests. The project will capitalise on brassicales seed lines (e.g. oil seed rape varieties) available at York, which have different levels of secondary compounds – the impacts of this variation for pests has not been examined yet is likely to be considerable. More importantly, the impacts of this variation are likely to vary in relation to abiotic growth conditions (temperature and CO2).

The project will interest someone wanting to carry out research on the ecological and biochemical impacts of climate change. The project will focus primarily on understanding mechanisms and consequences of the observed changes in host plant use by insects. The project will involve lab work, but there will also be some field work. Skills and experience will be gained in insect sampling and rearing, experimental design, statistics, and analysis of plant secondary compounds. The student will work in research labs of Jane Hill (working on ecological impacts of climate change) as well as the labs of Sue Hartley (York Environmental Sustainability Institute YESI; working on impacts of climate on crop plants).

Supervisors: Prof Jane Hill & Prof Sue Hartley

To discuss your suitability for this project please email: jane.hill@york.ac.uk

Please read the 'How to apply' tab before submitting your application.

 

 

 

Novel regulators of seedling growth. Supervisors: Prof Bob White, Dr Louise Jones & Prof Ian Graham

As populations increase, the need to improve crop yields is becoming increasingly urgent.  Levels of tRNA can strongly influence growth in some organisms by influencing rates of protein synthesis, but almost nothing is currently known about how tRNA expression is connected to the growth of plants.  Our project will characterize this fundamental issue to illuminate basic principles of growth control in plant seedlings.  It will combine molecular biology and genetic approaches to characterize tRNA gene regulation in terms of transcription factors and epigenetic changes.  It will also test whether raising tRNA expression can stimulate seedling growth.    

Supervisors: Prof Bob White, Dr Louise Jones & Prof Ian Graham

To discuss your suitability for this project please email: bob.white@york.ac.uk

Please read the 'How to apply' tab before submitting your application.