Projects that commenced in 2016

Bristol

Supervisors: Dr Eric Morgan (University of Bristol), Dr Christos Ioannou (University of Bristol)

Others in supervisory team/collaborators: Dr Colin Torney (University of Exeter)

Parasites cause massive losses to the sheep industry worldwide and have major detrimental effects on the welfare of animals. Overuse of drugs has led to resistance in a number of economically-important parasites, and a more sustainable approach of only treating highly infected individuals is advocated. However, assessing infection from laboratory-based measurements such as faecal egg counts is costly. This project will develop the use of Global Positioning System (GPS) collars and accelerometers to monitor sheep behaviour, in order to understand how space use is related to risk of infection, how space use changes with increased parasite load, and how parasite load affects movement and the ways in which individual sheep interact with one another. Finally, you will design and carry out controlled field experiments to test the effects of anti-parasite drugs on these parameters, to determine whether the effects of parasite load on behaviour can be reversed.

The project will focus on gastrointestinal nematodes such as Teladorsagia circumcincta, the liver fluke (whose snail intermediate host prefers wet environments), and ticks (which prefer edge habitat and rough grazing, and carry several important diseases). There will be large components of both fieldwork and data analysis, with significant support from all three supervisors. Pilot projects will build on existing studies relating habitat use to tick and nematode risk, and on use of GPS data in animal behaviour studies.

The student will gain training in a wide range of skills, including assessment of welfare indicators and parasite load, sampling microhabitats to effectively map at-risk areas in fields, field observations of behaviour to corroborate GPS data, data analysis to extract potential behavioural indicators from GPS coordinate data, and statistical analysis to explore how parasite load is associated with space use and movement.

There is little utilisation of behavioural assays in livestock husbandry to assess infection and its consequences, despite the numerous effects parasites have on animal behaviour in a range of species. This project will break new ground by harnessing technology to monitor behaviour and assess the interaction between behaviour and parasite infection. A major long-term goal of the project is to develop behavioural indicators for infection risk and parasite load which can be utilised in real-world settings.

Supervisors: Prof Claire Grierson (University of Bristol), Prof Timothy Quine (University of Exeter)

Others in supervisory team/collaborators: Prof Tannimola Liverpool (University of Bristol), Dr Isaac Chenchiah (University of Bristol)

Humans have degraded almost a quarter of vegetated land on earth, most by soil erosion. Soil loss on conventionally managed agricultural land dwarfs soil production with around 12 million fertile hectares lost annually. Plant roots produce soil cohesion, retain soil on slopes and cycle nutrients into soils, which are amongst the largest carbon sinks on earth (Lal R, Science 304: 1623). However, we don’t know how roots stabilise soils; differences between species show that plant genes matter, but almost nothing is known about such genes. This ignorance could prove costly as population growth demands more food production. Climate change may compound the problem by bringing more frequent extreme weather likely to exacerbate soil loss.

In work funded by the Leverhulme Trust and SWBio DTP we have established methods to measure cohesion between Arabidopsis roots and soils. By comparing Arabidopsis mutants we have identified root traits that prevent uprooting and water erosion (two papers and a review in preparation). Our work to date identifies two important areas for further development: 1. Cohesion is a product of root-soil interaction and we need better understanding of the effectiveness of identified traits in a range of soils. 2. Plants adapt to their local environments and so far we have been testing laboratory strains, grown in compost for 60+ generations, that might have lost important traits for root-soil cohesion. The diversity of traits in natural soils is not known nor is the extent to which root traits reflect the ‘native’ soil.

This PhD project will address these issues. The student will discover how root-soil cohesion works in a wide range of soil types, and at the same time identify and rank the importance of any root traits we might have missed. The results will identify root traits that contribute to root-soil cohesion across a wide range of soil types along with mechanisms by which plants have adapted to specific properties of their local soils.

Supervisors: Prof Wendy Gibson (University of Bristol), Dr Jamie Stevens (University of Exeter)

Others in supervisory team/collaborators: Prof Mick Bailey (University of Bristol), Prof Mark Carrington (University of Cambridge)

Tsetse-transmitted trypanosomes are the causative organisms of trypanosomiasis in livestock, a debilitating and economically costly disease in sub-Saharan Africa. Work in Bristol has recently shown that a previously unidentified trypanosome culture is in fact an isolate of a long-lost trypanosome, Trypanosoma suis, previously reported as a pathogen of pigs in Africa (Hutchinson & Gibson “Rediscovery of Trypanosoma (Pycnomonas) suis, a tsetse-transmitted trypanosome closely related to T. brucei”, submitted). Little is known about this trypanosome, as there has been no lab isolate for the past 60 years, but nevertheless it occupies a key place in the evolutionary history of Trypanosoma brucei and related pathogens of humans and livestock.

In this project, the student will have the unique opportunity to explore the biology of T. suis, drawing on genomic and transcriptomic data resources compiled by our collaborator at Cambridge University. During the project, the student will train in both parasitology and molecular biology approaches and become expert in a number of parasitological, imaging, immunocytochemistry and molecular cell biology techniques.

Supervisors: Prof Alistair Hetherington (University of Bristol), Prof Nick Smirnoff (University of Exeter)

Others in supervisory team/collaborators: Dr Ant Dodd (University of Bristol), Prof Mervyn Miles FRS (University of Bristol)

Plants have evolved mechanisms that allow then to adapt to changing environmental conditions. At the heart of these responses are systems that enable plants to detect changes in their environment and then to formulate the appropriate response to the changed conditions. At the level of the single cell changes are detected by receptors and then a complex intracellular machinery is responsible for the elicitation of the appropriate intracellular response. This process is known as stimulus-response coupling (or intracellular signalling). Of central importance in this machinery are Reactive Oxygen Species (ROS). When a cell reacts to an external stimulus the concentration of the ROS inside the cell increases. This acts as an intermediate in the generation of the final response. The ubiquity of ROS as intermediaries involved in the responses to a plethora of different stimuli raises an important question and this is; how can the increase in ROS elicit specific responses?

Stomata are pores on the surfaces of leaves that open and close in response to changing environmental conditions. The stomatal pore is formed by two guard cells. When these shrink the pore closes whereas swelling results in opening. Stomata are important because they control carbon dioxide uptake and water loss. In guard cells stimuli that bring about swelling (opening) or closure (shrinking) both use intracellular signalling pathways that involve an increase in ROS. How does this work? Unravelling how response specificity is controlled in a single cell is one of the big and unresolved questions in plant cell signalling.

Previously making measurements of ROS inside cells has been problematic, however here we are making use of step-change advances in technology developed in one of our labs to provide an unprecedented understanding of ROS dynamics in single cells. We believe that we have an international lead in this area, accordingly this is a very timely project bringing together the new technology from Exeter and the biological system (stomata) in Bristol to find answers to a major unresolved question. Our hypothesis, is that different stimuli generate unique patterns of ROS inside cells. We call these ROS signatures. These are then decoded by the intracellular machinery inside the cell to produce the specific response. In this application, we will use our new technology to test this hypothesis. We will carry out these experiments in both Arabidopsis and cereals and in evolutionary more basal lineages. Our cereal work has the potential to identify new targets for agronomic improvement.

Cardiff

Supervisors: Prof William Symondson (Cardiff University), Dr Ian Vaughan (Cardiff University)

Others in supervisory team/collaborators: Dr Pablo Orozco-ter Wengel (Cardiff University), Dr Carsten Muller (Cardiff University), Dr James R Bell (Rothamsted Research)

Spiders are major predators of aphids (and other pests) in cereal crops and are an essential element of pest control in low-input and organic agriculture. However, their economic value to farmers is affected by their density and relative predation rates on pest and non-pest insects. It has been demonstrated in the lab that predators can exercise nutrient-specific foraging to balance their diets (Mayntz et al., Science 2005). Thus, if they have been eating sugar-rich aphids they may preferentially increase predation on protein-rich Collembola or flies. Spiders cannot survive on aphids alone and agriculturalists require guidance on the need to preserve non-aphid prey within crops. However, nutrient-specific foraging has never been demonstrated in the field. Our aim will be to compare what is available to the spiders with what the spiders have eaten. Major nutrients will be analysed for common prey (e.g. Hawley et al., PlosOne 2014). We will analyse diets of spiders using molecular methods then compare what is available with what is eaten, looking for deviations from random feeding that balance their nutrient intake. Mesocosm experiments, informed by prey densities in the field and spider diets, will confirm whether nutrient-specific foraging, rather than other factors, is regulating prey choices.

Exeter

Supervisors: Prof Ken Haynes (University of Exeter), Dr Jason Rudd (Rothamsted Research)

Others in supervisory team/collaborators: Dr Steve Bates (University of Exeter), Dr Mike Deeks (University of Exeter)

Septoria tritici blotch (STB) is the most economically important foliar disease of wheat in the UK and Western Europe, and is caused by the fungus Zymoseptoria tritici. The developmental program that underpins Z. tritici infection has been partially characterized at the molecular and cellular level, but the early events in infection, particularly relating to autophagic cell death and loss/retention of chromosomes remain largely un-explored. The principle aims of this project are to close these knowledge gaps. Specifically the project will define the role that autophagy genes play in the development of Z. tritici pycnidiospores as they germinate on, and initiate infection in compatible wheat cultivars. Once these roles have been mechanistically defined using a combination of advanced cell imaging, controlled expression and mutant analysis the impact on the maintenance of the eight dispensible chromosomes in the Z. triticigenome will be investigated. These experiments will generate novel biological understanding, elucidating critical determinants that are required for initiation of infection, that can be translated into applied outcomes, in particular the discovery of targets for novel fungicide development.

The student will gain experience of cutting edge molecular, cellular and fungal biology, alongside advanced in plantaimaging of infection. They will be trained in all aspects of host-pathogen interaction and will work at two world class research centres.

Supervisors: Dr Dan Bebber (University of Exeter), Prof Sarah Gurr (University of Exeter/Rothamsted Research)

Others in supervisory team/collaborators: Dr Helen Fones (University of Exeter)

Fungal plant pathogens threaten global food security. Crop infection risk is determined in part by temperature and moisture availability, and climate change will alter distributions of both crops and their pathogens. Mathematical models of changing pathogen distributions often implicitly assume that fungi will respond to temperature in the future much as they do now, with no evolution to changing conditions. However, a small amount of existing research has shown that fungi can acclimatize and evolve rapidly to withstand warming. This studentship will combine laboratory experiments and modelling to investigate acclimation and adaptation of plant pathogenic fungi to temperature increases:

1. What is known about variation fungal temperature tolerance? The student will conduct a detailed literature survey of fungal pathogen temperature responses, comparing these to the temperature tolerances of the host crops and statistically investigating the relationships between temperature tolerance, host specificity, biogeography, and evolutionary relationships among fungi.

2. How does Zymoseptoria tritici respond to increasing culture temperatures in the lab? The student will investigate the changes undergone by fungal cultures, assessing molecular and morphological aspects of fungal biology.

3. How do fungal pathogens adapt to temperature variation in the wild? The student will work with Z. tritici isolates originating from a range of climates around the world, and develop temperature response curves (TRCs) from in vitro growth rates. These will be compared with temperature acclimated fungi to determine how in vitro acclimated cultures relate to those which have evolved in the wild.

4. What are the genomic signatures of temperature adaptation? The student will sequence the genomes of wild adapted isolates will be used to determine how Z. tritici has evolved in the wild to grow under different climates. You will compare these results to those obtained temperature acclimated strains in vitro, to determine whether physiological and evolutionary responses high temperatures involve the same pathways.

5. Is there a trade-off between temperature acclimation and virulence? Evolutionary theory predicts a trade-off between responses to different types of stress. For example, a pathogen responding to high temperature might be less able to infect the host plant. The student will test whether fungal isolates that have been acclimated to grow at higher temperatures retain virulence on wheat.

Through this doctorate the student will receive training in statistical analysis, ecological and evolutionary theory, plant pathology, microbiology, fundamental lab skills, genomics and bioinformatics, as well has making an important contribution to the science of climate change and global food security.

Supervisors: Prof Richard ffrench-Constant (University of Exeter), Dr Alistair Miller (Darrhouse Chemical Company)

Others in supervisory team/collaborators: Prof Chris Bass (University of Exeter), Prof Nina Wedell (University of Exeter), Prof David Hosken (University of Exeter), Prof Helge Bode (University of Frankfurt)

The current use of insecticides in crop protection is limited both by their safety and by concerns about insect resistance. One of the primary reasons for insecticide resistance is that available chemicals belong to very few major chemical classes (e.g. OP’s, carbamates, pyrethroids and neonicotinoids) and can therefore all end up acting on a rather limited number of targets or receptors. This project is designed to take an insecticidal natural product from the bacterium Xenorhabdus and to use this as a starting point for the development of a novel class of insecticidal chemistry. This project is a CASE partnership between Darr House Chemical, a small chemical company based outside of Exeter, with the Biosciences Department on the Penryn Campus of the University of Exeter. The student will gain direct experience in subjects ranging from chemical synthesis and design to the molecular biology of insecticide resistance. We will make extensive use of in house resistant stains of pest insects in order to guarantee that any novel compounds overcome existing mechanisms in multiply resistant aphids and whitefly. The project will be based in the laboratories of Professors Richard ffrench-Constant and Chris Bass at Penryn where the majority of the screening and structure/activity work will be performed.. The student will gain experience in 1) chemical design and synthesis, 2) drug and pesticide screening against a range of cell types and whole insects, 3) the molecular biology of drug metabolism and resistance.

Rothamsted

Supervisors: Prof Kim Hammond-Kosack (Rothamsted Research), Dr Michael Deeks (University of Exeter)

Others in supervisory team/collaborators: Prof Nick Talbot (University of Exeter), Dr Christine Faulkner (John Innes Centre), Dr Smita Kurup (Rothamsted Research), Dr Wing-Sham Lee (Rothamsted Research), Dr Martin Urban (Rothamsted Research)

Climatic, environmental and societal changes led to the evolution of novel crop pathogens. Many new pathogen problems have evolved which now regularly threaten global crop production. Phytopathogenic species which cause crop plant diseases are annually responsible for the loss of ~15% of total crop yield globally and are therefore a serious threat to global food security. Particularly serious are Fusarium ear blight (FEB)/head scab disease caused by cereal infecting Fusaria fungi (www.scabusa.org) (Figure) and Zymoseptoria tritici infections in wheat crops (Dean (2012) Molecular Plant Pathology 13, 414–430), both will be studied in this PhD project. Figure A Fusarium decimated wheat crop

The main scientific aims of this project are (A) to investigate both the cellular and molecular mechanisms in wheat required for the transition of Fusarium graminearum hyphae from apoplastic to plasmodesmatal growth (Brown (2010), Fungal Biology 114, 555-571) and (B) to explore the functional role(s) of specific plasmodesmata associated wheat proteins (Faulkner (2013) PNAS, 110, 9166-9170). To achieve the project aims the student will learn how to use a range of existing tools (fungal reporter strains, wheat transformants), established techniques (RNA seq analyses, light/UV/confocal microscopy, Virus Induced Gene Silencing (VIGS) (Lee (2012) Plant Physiology 160, 582-590) and emerging technologies (genome editing). They will also be trained in the use of bespoke software to quantify and mathematically model the in vivo fungal-plant image datasets acquired from their detailed microscopy studies.

Supervisors: Prof Nigel Halford (Rothamsted Research), Dhan Bhandari (HGCA), Prof Keith Edwards (University of Bristol)

Others in supervisory team/collaborators: Prof Huw Jones (Rothamsted Research), Dr Chris Tapsell (KWS UK Ltd), Ed Byrne (KWS UK Ltd), Richard Jennaway (Saaten Union), Celia Bequain (RAGT), Ian Foot (Limagrain), David Feuerhelm (Syngenta)

Acrylamide (C3H5NO), which is a Class 2a carcinogen, is a processing contaminant that forms from free asparagine and sugars during high-temperature cooking and processing. Baked cereal products are major contributors to dietary intake of acrylamide in Europe, with bread alone accounting for 11 to 32 %. Decreasing the free asparagine concentration of wheat grains would reduce the potential for acrylamide formation and this is important because the presence of acrylamide in food is now a major problem for the food industry.

The aim of this project is to use the latest genome editing techniques to deliver very low asparagine wheat genotypes for incorporation into breeding programmes. The project will exploit tools, resources and knowledge that have already been generated, including cloned genes, monoclonal antibodies and mathematical models describing asparagine metabolism. Wheat plants will be created in which the asparagine synthetase gene that is predominantly expressed in the grain has been knocked out. The advantage of using this technique is that those regulatory authorities around the world that have issued an opinion have classified genome-edited plants as non-GM.

The project is backed by the UK’s major wheat breeders and the Agriculture and Horticulture Development Board, and the student will gain expertise in gene cloning, designing and making gene constructs, transgenic wheat, back-crossing, and the biochemical and molecular analysis of genome-edited plants. The Halford team at Rothamsted Research are leaders in research into reducing the acrylamide-forming potential of major crops and the genetic and environmental factors that influence asparagine metabolism, while the Cereal Transformation team led by Huw Jones and University of Bristol supervisor Keith Edwards have experience of applying genome editing techniques successfully in wheat.