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Plant Molecular Sciences Masters by Research

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Plant Molecular Sciences Masters by Research

Projects and Supervisors

Choose one of the projects from the list below.

Dr Laurence Bindschedler
How does barley powdery mildew interact at the protein level to successfully invade its host?

Pathogens secrete small proteins called effectors or virulence factors which are important for the successful invasion of the host. These effectors act by compromising the host immunity. Powdery mildews are economically important obligate fungal pathogens of cereals such as wheat and barley. Barley powdery mildew expresses and secretes many small unknown proteins of unknown functions, as well as a protease and glucosidases at the early stage of infection. To understand their function, we will be addressing one or some of the following questions:

When and where are they expressed?

Which barley proteins do they target?

Are they species specific?

Are they required for a successful infection?

Molecular and proteomic approaches will be used to investigate the role of powdery mildew effector proteins of this plant pathogen during infection of barley by its powdery mildew.

RNAi in planta to control diseases caused by obligate fungi in cereal crops

The aim of this project is to develop high output workflow for gene silencing of plant pathogenic fungi with an ultimate goal of controlling plant diseases.

RNA interference (RNAi) is a powerful technique to investigate gene function by down regulating the expression of a particular gene in vivo (i.e. gene silencing).

Large scale RNAi strategies were possible through the design of synthetic siRNAs in mammalian systems or artificial microRNAs in plants but depend on cloning and protoplasts production.

Newer methods to adapt RNAi to plant systems have emerged using either cell permeable peptides to use direct siRNA or oligodeoxynucleotides (ODN) molecules uptake in whole plants or leaves.

Research pages - Dr Bindschedler

Professor Laci Bogre
Balancing Assimilates for plant growth, cell proliferation and productivity

Plant growth and crop productivity is intimately linked to the efficiency of light capture and to the balanced storage and utilisation of assimilates. The evolutionary conserved TOR-S6K signalling pathway functions to adjust the rate of protein synthesis to demands (Deprost et al. (2007) EMBO Rep 8:864-870.).

Cell proliferation is repressed upon carbon starvation, and we have shown that S6K1 is playing a role in this process (Henriques et al. (2010) EMBO J 29:2979-93.). We have also shown that exposure of etiolated seedlings to light rapidly revert starvation and leads to activation of protein synthesis and cell proliferation in shoot apex.

Light has a direct input into cell proliferation through DET1 and COP1 which regulate the balance between transcriptional activator/repressor; E2FB/E2FC (Lopez et al (2008) Plant Cell 20:947-68.). Cell proliferation adjusted to available sucrose through regulating the expression, translation and protein stability of D-type cyclins and so RBR phosphorylation and leads to the release of E2FB to activate proliferation (Magyar et al (2012) EMBO J. 31:1480-93.).

On the other hand, E2FA forms a stable repressor complex with RBR to maintain the meristem, while E2FC appears to be involved in induction of genes involved in metabolism, light and circadian rhythm (deJager et al. (2009) PMB 71(4-5):345-65.). The central question of this project: how carbon balance is connected to the regulation of growth and cell proliferation.

How plant growth is adopted to drought conditions

One major consequence of the global changes in climate is an uneven distribution of freshwater, leading to drought in large areas worldwide. This has already had a strong influence on agricultural productivity.

Our current understanding of plant adaptation to drought stress is limited to survival mechanisms, but little is known about how mild drought condition restrains plant productivity and yield. We have discovered a drought induced MAPK signalling pathway that restrains plant growth through multiple mechanisms; i) by regulation auxin transport, ii) regulating cell proliferation.

The overall aim of the proposed research is to identify cell cycle-regulatory targets of the drought-responsive MAPK signaling pathway, and link these to the growth adaptation of plants under drought stress conditions. To do this we will perform: (ii) computational predictions of MAPK substrates involved in cell cycle regulation, (iii) targeted approaches to test MAPK phosphorylation of key regulators in plant growth regulation, the RBR transcriptional repressor complex.

Research pages - Professor Bogre

Dr Paul Devlin
Next generation sequencing-based analysis secondary metabolite production pathways in basil

Basil is a culinary herb prized for its flavour and aroma. These characteristics are determined by the production of an array of secondary metabolites. We are interested in the environmental regulation of those pathways. We have been using a next generation, high-output RNA sequencing approach to generate RNAseq data from basil plants grown under different environmental conditions. Our aim is to examine the environmental effects on the expression of genes involved in secondary metabolite production pathways. By understanding more about these pathways and their environmental responsiveness at the molecular level, it is hoped that we can improve secondary metabolite production by modifying growing conditions.

This project will provide training in RNA-seq data analysis in order to examine patterns of differential gene expression. It will also involve quantitative RT-PCR-based confirmation of this pathway analysis and testing of the effectiveness of predictions for improved growing conditions

Next generation sequencing-based analysis of the effects of farming practice on the plant microbial flora

Healthy plants, like all higher organisms, host an extensive commensal microbial community or microbiome. Non-pathogenic microbes are tolerated and in many cases benefit the host. In plants, the leaf microbiome, the phyllosphere, contains a wide range of bacterial and fungal species, including some that have been shown to play an important role in disease prevention. Changes in the microbiome can, therefore, have important effects on the disease susceptibility of the host. We have been using high-output, next generation sequencing technology to analyse the impact of plant disease responses on the microbiome. Direct community sequencing-based approaches negate the need to culture microbes and allow taxonomic diversity of communities as a whole to be compared. Agricultural treatments are also likely to have a significant impact on the ecology of the plant phyllosphere. This project will use next generation sequencing technology to examine the effects of treatments such as pesticide, bactericide, fungicide, and even herbicide and fertiliser treatments on the phyllosphere microbial community. It will also examine the potential for probiotic treatment / microbiota transfer to help restore phyllosphere microbial homeostasis.

Research pages - Dr Paul Devlin

Professor Alessandra Devoto
Sustainable biomass and high-value chemical production and stress responses in crops

This study aims to investigate several aspects of the control of plant defences and to identify environmentally friendly forms of plant protectants, leading to enhanced crop yields. We aim to explain host processes and components required for the growth and reproduction of different plant microbes to uncouple stress-induced growth in crop species. Investigating more thoroughly and pinpointing what an invading microorganism does to be able to bypass or inactivate the host plant defences will open up the possibility to engineer crops to gain ‘natural immunity’. The expression of molecular markers such as genes expressed during pathogenesis will be characterised. We will also explain host processes linked with microbial growth to uncover cellular and metabolic changes associated with their demands (Noir et al, 2013, Plant Physiology 161: 1930-1951). This research will also further our understanding of biomass production and its regulation in response to stress to improve cell wall accessibility in biofuel feedstocks from different plants (Cook C, Devoto A, 2011, J Sci Food Agr, 91:1729-1732). The project will use high-output functional genomics including molecular and cell biology techniques including functional transient assays as well as bioinformatics.

Novel biotechnological routes to discovering phytopharmaceuticals in plants

The plant hormone jasmonic acid induces the biosynthesis of defence proteins and protective secondary metabolites. Pathways with potential for the production of therapeutic drugs will be manipulated with the dual aim of developing a greater understanding of the metabolism involved, that is often related to plant defence, and to develop small molecules or precursors for new medicines. Success in manipulating the targeted metabolic pathways will be analysed through a novel functional screening system. The analysis of diverse plant lines will improve the understanding of key pathways leading to the production of economically important compounds acting as toxins, antimalarial, or antineoplastic drugs in planta or even as important nutrients. The project offers the opportunity to become familiar with approaches and techniques of wide applicability such as functional genomics and transcriptomics as well as molecular biology and protein engineering. We will establish the role of newly identified molecular components of jasmonate (JA)-mediated stress and development (Noir et al, 2013, Plant Physiology 161: 1930-1951; Balbi and Devoto, 2008, New Phytologist, 177: 301-318). This project will contribute to identifying the link between plant growth and responses to stress and will lead to the discovery of regulators with the potential to engineer stress signalling pathways.

Research pages - Professor Devoto

Professor Paul Fraser
Industrial Biotechnology: A synthetic Biology approach to the production of high value isoprenoids in renewable hosts

Plant and microbial natural products have been utilised by human civilisation for millennia, providing vital medicines and essential dietary components. More recently bioactive compounds from plant sources have been used in cosmetics, as health supplements and are important components of food and feedstuffs. Phytochemicals are also important industrial raw materials and high-value fine chemicals. Despite the significant investments made in combinatory chemical synthesis, these platforms have not delivered the desperately needed new activities and/or sources of complex structures found in nature. Chemical synthesis is also expensive and typically associated with chemical refineries using non-renewable energy sources and byproducts.

Terpenoids or isoprenoids are a class of compounds within which specific compounds have anti-cancer activity, confer health benefits, are natural colorants, and feed supplements. The present markets for isoprenoid compounds such as ketocarotenoids which are natural colorants and antioxidants are worth over $1 billion per annum, with demand far exceeding supply (Marz, 2006, Business report. Global Market for carotenoids, Norwalk CT, USA: Business Communications Company).

In the proposed project the applicant will (i) characterise existing transgenic plants and microorganisms producing high value bioactive natural products using modern omic technologies and (ii) generated and evaluate new biosources of these compounds using synthetic biology approaches.

Characterisation of staple crops (banana, yam, sweet potato and cassava) by metabolite profiling

Banana (Musa spp.), Cassava, Yam and Sweet potato are one of the top ten staple foods in the developing world and a target for international development to genetically enhance these crops. The proposed project will augment on-going plant breeding programmes in Africa, Asia and South America, designed to improve consumer traits in banana fruit. The applicant will perform metabolite profiling on well characterised segregating populations and integrate this metabolite information with genetic data. QTL underlying traits and candidate genes will then be characterised in transient and other fruit systems. The applicant will be provided with a unique opportunity to interact with research programmes aimed at combating food insecurity and poverty in developing countries.

Research pages - Professor Fraser
Project pages - and

Professor Gerhard Leubner
Molecular and hormonal mechanisms underpinning seed technologies applied to crop, flower and vegetable seeds by industry

The aim of this project is to determine the mechanisms which are underlying seed enhancement technologies to achieve rapid and uniform germination and seedling establishment. These technologies include seed priming, sorting, pelleting and the inclusion of various additives. Examples for the effects include the release of seed dormancy of vegetable and flower seeds, the control of aging processes during sugarbeet and onion seed storage and the benefits of priming to improve abiotic stress responses and vigour during germination and pre-emergence seedling growth (see projects on our PURE website below). The underlying mechanisms include regulation by altered hormonal contents and signalling and epigenetic changes leading to distinct transcriptome expression patterns. Very little is known about these mechanisms and therefore the optimisation of the seed enhancement technologies and their application to specific crop species is hampered. In the project we will investigate crop seed enhancement technologies with modern molecular, biochemical, microscopical and biophysical methods to understand how embryo growth, dormancy release and germination speed, uniformity and vigour are improved. This project is at the interface of fundamental and applied seed biology and engineering.

Molecular mechanisms of gene expression during weed seed dormancy, germination and persistence in the soil seed bank

The sustainable intensification of food production necessary to feed the world’s growing population will only be achievable if crop harvest losses due to heat stress and competition with weeds are minimised. About ten per cent of crop production is currently lost to weeds and this loss would be far greater without the use of herbicides. However, the continued effectiveness of herbicide technology is threatened by the rapid advance of weed biotypes that are resistant to herbicides. The problem of effective weed control is most severe in annual field crop systems and with annual weeds which emerge at the same time as the crop seedlings. These problem weeds owe their success, at least in part, to the formation of large and persistent soil seed banks. Thus there is considerable potential for novel weed control solutions through engaging a deeper understanding of the molecular mechanisms of weed seed germination and survival. In the project we will focus on hormone-related mechanisms which mediate the environmental responses of weed seeds. Seed hormones will be quantified and the expression of corresponding genes analysed in the seeds of a variety of noxious weeds and in response to temperature as environmental factor. This project is in collaboration with Syngenta and at the interface of fundamental and applied seed science.

Research pages - Professor Leubner

Project pages 'The Seed Biology Place'

Biopriming as a seed technology and its impacts on germination and seedling vigour

This project aims to investigate the interactions between bacterial endophytes and the seeds of high yielding crop species. Biopriming is a priming technology whereby seeds are hydrated and inoculated with a beneficial organism. Seed priming to modify hydration has been found to have several physiological benefits in the vegetable seed market such as increasing the uniformity and speed of germination. Biopriming however, builds upon this principal with the addition of a microbial inoculant. These are typically microorganisms that may confer benefits to the growing plant such as greater access to macro and micro-nutrients or host plant defence. This project will work with a specific nitrogen fixing bacterial endosymbiont and consider the impacts that seed inoculation with this bacteria on germination, seedling establishment and seed hormones on a range of plant species that exist in different agroecological niches. This project will utilise modern microbiological, microscopical, biochemical and hormone quantification techniques and is likely to work closely with industry partners, with the possibility of a short industry placement.

For enquiries about this Project in the Leubner laboratory, please contact Dr James Hourston.

Dr Enrique Lopez
Developmental biology of leaf initiation in the light

Leaves are light-capturing organs that develop from a group of “stem cells” (meristamatic cells) at the tip of plant shoots. The development of leaves initially involves active cell proliferation, followed by differentiation, and in dicot plants it occurs only in the light: light acts as a cell proliferation and development switch. We seek to understand how this takes place. This project will follow on from our previous studies, using the model plant Arabidopsis thaliana, that have shown that leaf initiation in the light coincides with (1) a substantial rearrangement of hormonal responses at the shoot meristem and (2) an activation of a “feast”, or repression of a “starvation” pathway. You will use existing or newly-isolated Arabidopsis mutants in these pathways, in an attempt to generate a mutant combination that exhibits de-repression of leaf initiation, or accelerated leaf growth in the light. You will select one element of this network to focus on. You will also attempt to connect these pathways to cell cycle activation. You will use molecular genotyping, microscopic image-analysis, and gene expression techniques

Genes involved in chloroplast biogenesis

Chloroplast build-up is also essential for the photosynthetic production that drives plant growth, and that ultimately produces our food. Chloroplasts are built primarily while meristematic cells differentiate into leaf mesophyll cells. Through mutant screens in the model plant Arabidopsis thaliana, we have identified in the past genes whose function is essential for chloroplast biogenesis, or whose dysfunction rescues prior defects in chloroplast development (positive elements or negative regulators of chloroplast biogenesis, respectively). In this project you will focus on one of these genes, confirm its subcellular localisation and examine potential mechanisms of action, through examination of molecular and cellular phenotypes of the mutants and through generation of plants with elevated levels of the selected gene.

Research pages - Dr Lopez

Dr Tony Stead
Providing better quality cut flowers

There are several stages, both pre- and post-harvest, which can adversely affect the quality of cut flowers purchased by the consumer. These range from the growing conditions, specialist post-harvest treatments, transport conditions, in-store treatment as well as the vase treatments in the home. Current projects are looking at the effect of light quality on pigmentation and flower opening, treatments to wash in-store buckets as well as the composition of the vase solution. We have a particular interest in Alstroemeria, Dahlia and roses; we are also studying chill-sensitivity in potted plants such as Phalenopsis

Improving the quality of culinary herbs

The benefits of healthy eating are well known, have you eaten your five portions of fruit and veg today? What is often overlooked is that herbs can provide a significant quantity of beneficial antioxidants or similar compounds. Ironically the consumer perception of which type of herb (pot-grown, cut leaf, dried etc) is best is usually wrong but it does indicate that improvements can be made to the quality of UK-grown pot herbs. These improvements relate to the growing conditions, particularly temperature, light quality and the presence of symbiotic mycorrhizae or other biostimulants. We are also concerned about improving chill tolerance in basil, and improving volatile levels produced by many culinary herbs.

Replacing peat in horticulture

Most potted plants (herbs and ornamentals) rely on peat-based composts although over 60 per cent of peat consumption is by amateur, not professional, growers nevertheless the Government has set targets for banning the use of peat due to its continued extraction being unsustainable and environmentally damaging, thus a replacement has to be found. We have been working with both commercial growers and the Royal Horticultural Society to try and find replacements for peat that do not compromise plant growth.

All of this research is applied but often involves explaining underlying mechanisms which has involved the use of microarrays and RNAseq to study gene expression studies as well as PCR techniques. Some work has involved microscopy using both light and electron microscopy. Some projects may have commercial sponsors that may contribute to the costs of the work and/or provide a small student bursary.

Research pages - Dr Stead

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