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Available Projects

We are always looking for enthusiastic students to join our projects, learn techniques and generate data for publications.

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Read through the available opportunities below, which can be tailored for:

Details of scholarships can be found here.  Please contact the relevant supervisors to discuss options for you.

  • Improving pathogen resistance in barley plants

    Description
    Barley is the fifth largest crop in the world. It is used for human food, animal feed and malting and brewing. Numerous genes are involved in plant growth and development, from the initial stages of grain germination through to the senescence of the plant prior to harvest.

    This project will focus on grain and leaf resistance to pathogen attacks, specifically investigating:

    • The location and amounts of anti-microbial hordatines in grain tissues during germination using a newly developed chromatographic technique
    • The timing and roles of jasmonate hormones in directing plant resistance
    • Possibly, the effect of foliar application of hordatines on barley leaf resistance to Blumeria graminis infection
    • Genes that drive barley resistance, with the overall aim to find breeding targets using existing RNAseq datasets developed from barley grain tissues during development and germination.

    Techniques learnt
    Experimental design; plant tissue harvesting and sample preparation; high performance liquid chromatography (HPLC); possibly, barley plant growth, infection, and subsequent isolation of epidermal layers; correlation of results with gene expression from existing RNAseq datasets; primer design for quantitative PCR analysis.

    Supervisors
    Dr Alan Little Dr Helen Collins and Dr Natalie Betts
    Dr Alan LittleDr Helen CollinsDr Natalie Betts
  • Fungal penetration resistance in barley

    In plants, the cell walls are one of the first lines of defence protecting the cell from successful invasion and are a major factor in basal host resistance against fungal pathogens. As a defence response, plants reinforce the cell wall near the site of penetration by producing a dome-shaped apposition (papilla) between the epidermal wall and the plasma membrane. The polysaccharide composition of papillae that have been effective in preventing penetration by Blumeria graminis f. sp. hordei (Bgh) are traditionally believed to contain callose as the main polysaccharide component. However, recent evidence presented by our group demonstrated that effective papillae that are successful in preventing the penetration attempts of Bgh contain significantly higher concentrations of callose, arabinoxylan and cellulose (Chowdhury et al., 2014).

    The current methods utilised for screening a cultivar’s susceptibility to fungal infection involves standard disease resistance ratings by macroscopic and microscopic assays. This is time and labour intensive with long times required to generate symptoms on the leaves. The results can also be inaccurate due to the inherent variability of a subjective disease rating scale. This project aims to develop a quick and robust PCR method for quantitating the relative susceptibility of a barley cultivar to penetration by the powdery mildew causal agent, Blumeria graminis f. sp. hordei (Bgh). Once developed the assay will be utilised in a screen of barley germplasm and genetic analysis of potential resistance loci.

    Techniques learnt
    Fungal infection assays, RNA extraction, Quantitative real time PCR.

    Supervisors
    Dr Alan Little and Dr Neil Shirley
    Dr Alan LittleDr Neil Shirley
  • Design of biomimetic coatings to understand plant-pathogen relations

    Description
    Plant fungal pathogens have evolved highly sophisticated ways to infect crops and therefore are a threat to global food supply.  On surfaces such as leaves, they first adhere to the surface and, interestingly, seem to know how to grow directionally towards ideal locations for infection before beginning surface penetration. If it were possible to better understand how the fungus senses and responds to the physical and chemical cues present on leaf surfaces, then we could develop strategies for interrupting infection, or develop plants which prevent adhesion or conceal inductive cues.

    We propose that artificial surfaces can be constructed to model natural leaf surfaces. By designing surfaces with well-defined chemical and physical properties to which the fungus can respond, we will be able to understand the essential triggers for infection. Additionally, studying the adhesion on surfaces will allow us to understand how secreted chemicals prepare the surface before infection. The overall aim is to replicate essential components of the leaf and assemble these into a biomimetic model.

    The goal of this research project is to make biomimetic surface coatings and investigate their biological response. This will involve using surface coating methods on materials such as glass slides, and to visualise the fungi using microscopy. This will provide an opportunity to learn about novel polymerisation techniques, characterisation of surfaces using surface analysis, and to visualise their biological effect.

    Techniques learnt
    Surface coating and analytical techniques, Microscopy..

    Supervisors
    Dr Bryan Coad and Dr Alan Little
    Dr Bryan Coad
  • Characterising the jasmonate hormones in barley, and how they affect beer

    Description
    Hormones, such as jasmonates, drive many physiological processes during plant development and response to environmental stresses. In barley, jasmonates also regulate the lipoxygenase (lox) pathway, which can affect beer taste and foaming.

    This project will:

    • Identify genes involved in jasmonate biosynthesis from the recently sequenced barley genome
    • Determine their spatial and temporal patterns of expression from a new barley tissue series using quantitative PCR (qPCR)
    • Examine biochemical profiles (LC/MS) of barley, malt and spent grain samples from a brewery to find jasmonate products
    • Develop a new barley tissue series using lox mutant lines to examine changes jasmonate biosynthetic gene transcription

    Techniques learnt
    Experimental design; plant tissue harvesting and sample preparation; high performance liquid chromatography (HPLC); possibly, barley plant growth, infection, and subsequent isolation of epidermal layers; correlation of results with gene expression from existing RNAseq datasets; primer design for quantitative PCR analysis.

    Supervisors
    Dr Helen Collins and Dr Natalie Betts
    Dr Helen CollinsDr Natalie Betts
  • Structural studies of cell wall proteins involved during pathogenesis

    Description

    Fungi and oomycetes are notorious pathogens responsible for infections in plant particularly of agricultural importance. Among different diseases, the late blight disease of potato and downy mildew of grape are examples of infections in plant caused by these pathogens. Chitin is one of the important cell wall components of fungi and oomycetes, which is not common in other plant species. This enables us to target chitin synthesis pathway as an attractive drug target.

    Chitin Synthases (CHSs) are transmembrane cell wall proteins which are responsible for the synthesis of chitin, but the molecular mechanism is not clearly understood. The molecular structure of CHSs will significantly contribute in understanding the underlying mechanism of chitin synthesis as well as designing inhibitors for this pathway. In this project, we will study the molecular structure of CHSs using Ion Mobility Mass Spectrometry as well as X-ray Crystallography.

    Techniques learnt

    Protein expression and purification, Protein crystallization, Ion Mobility Mass Spectrometry, X-ray Crystallography, Protein structure determination.

    Supervisors
    Dr M Obayed Ullah and Professor Vincent Bulone
    Dr M Obayed UllahProfessor Vincent Bulone
  • Modulation of the plant defence response by the fungal extracellular matrix
    Description
    Whilst fungi have evolved carbohydrate structures to allow quick and reliable adhesion to the plant surface, the plant host has adapted to detect specific carbohydrate epitopes of the extracellular matrix (ECM), leading to activation of its innate immune response. Chitin- and glucan-based oligosaccharides common to all fungal cell walls act as key elicitors of the defence response; however, these molecules are located at the innermost layer of the fungal cell wall and cannot be readily detected by the plant unless significant damage has already been made to the pathogen cell wall. In contrast, the carbohydrates of the fungal ECM are secreted by the conidia within minutes of landing on the plant providing the host with a freely available mixture of potential elicitors. Preliminary data from our collaborators show evidence that carbohydrate fractions from our model system are capable of activating the defence response of economically important crops, thereby providing new promising targets for further research. This project will aim to collect and screen fungal ECM fractions for their ability to activate the plant defence response..

    Techniques learnt
    Fungal pathology, Cell wall biochemistry.

    Supervisors
    Dr Alan Little and Professor Vincent Bulone
    Dr Alan LittleProfessor Vincent Bulone
  • Genomic analysis of fungal nucleotide sugar interconverting enzymes

    Description
    The fungal cell wall is perhaps the most ideal target for the treatment of fungal pathogens. The fungal cell wall represents a considerable metabolic investment as it accounts for 15–30% of the cellular biomass. It plays such a momentous role to survival and maintaining homeostasis that up to 20% of genes in the fungal genome are associated with cell wall biogenesis. The enzymes and signal transduction pathways that govern the synthesis of these cell wall components are prime targets for antifungal drugs. Knowledge of the cell wall composition and its biosynthesis will allow more targeted and tailored approaches towards disease control.

    To date, only a small percentage of fungal cell walls have been characterised. The ability of fungi to generate the necessary sugar nucleotide substrates for the synthesis of various cell wall components is determined by the presence of the nucleotide sugar interconverting enzymes. This project aims to characterise the distribution of each nucleotide sugar interconverting enzyme family across the available fungal genomes that have been fully sequenced. In doing so, we will generate a predictive map of what sugars each fungal species is capable of making and potentially incorporating into its cell wall.

    Techniques learnt
    Bioinformatics, Cell wall biochemistry, Fungal pathology.

    Supervisors
    Dr Alan Little and Dr Julian Schwerdt
    Dr Alan LittleDr Julian Schwerdt
  • Characterisation of the fungal extracellular matrix and its role in adhesion

    Description
    Foliar pathogens are commonly dispersed in wind and need to adhere to the plant surface to begin the infection process. Once a fungal conidium lands on a leaf, a thin extracellular matrix is secreted to rapidly establish a strong connection to the plant surface. If adhesion is unsuccessful, the conidia cannot penetrate the plant host and will be removed by wind and rain. The composition of fungal adhesive matrices has only been partially deduced. Plant/fungal interactions can be disrupted by compounds that block adhesion or by enzymes that degrade the adhesive. Glycoproteins appear to play a key role in the fungal adhesion to the leaf surface. However, their identity and mode of action have not been determined and the glycan structures attached to these proteins have not been characterised. New technologies for genome editing and single molecule imaging will contribute to a better understanding of fungal adhesion, but progress will be limited without a fundamental understanding of the components involved.

    Techniques learnt
    Cell wall biochemistry, Fungal pathology.

    Supervisors
    Dr Alan Little, Dr Bryan Coad
    and Professor Vincent Bulone
    Dr Alan LittleDr Bryan CoadProfessor Vincent Bulone
  • The role of cuticular leaf wax during fungal adhesion

    Foliar pathogens are commonly dispersed in wind and need to adhere to the plant surface to begin the infection process. Once a fungal conidium lands on a leaf, a thin extracellular matrix is secreted to rapidly establish a strong connection to the plant surface. If adhesion is unsuccessful, the conidia cannot penetrate the plant host and will be removed by wind and rain. The interaction between the fungal conidium and the leaf surface first occurs with the cuticular leaf wax. The chemical composition and surface structure of the cuticular wax layer of the leaf has the potential to alter the chances of a successful fungal infection.

    This project will aim to generate artificial surfaces containing variable amounts of cuticular leaf wax components to determine their role in the fungal adhesion process. This will involve using surface coating methods on materials such as glass slides, and to visualise the fungi using microscopy. This will provide an opportunity to learn about novel polymerisation techniques, characterisation of surfaces using surface analysis, and to visualise their biological effect.

    Techniques learnt
    Surface coating and analytical techniques, Fungal pathology, Microscopy.

    Supervisors
    Dr Alan Little and Dr Bryan Coad
    Dr Alan LittleDr Bryan Coad
  • Analysis of fungal conidia development and synthesis of the extracellular matrix

    Description
    The powdery mildew (Blumeria graminis f. sp. hordei, Bgh) extracellular matrix (ECM) is secreted within minutes of host surface recognition, suggesting that fungal ECM components are synthesised and stored in the conidia prior to their release from the developing conidiophore. This hypothesis is supported by studies in Magnaporthe oryzae, where stored deposits of fungal ECM materials could be observed at the tip of fully matured conidia Conidia of Bgh develop and mature at the end of the asexual life cycle and can be seen protruding from the surface of the leaf in a linear chain of up to 10 conidial cells. Conidial cells begin as a division of the generative cell near the surface of the leaf. The generative cell elongates and divides via septation. Conidia mature progressively toward the tip of the conidiophore and are released when the septum has constricted fully. This system provides the perfect linear timeline of conidial development to observe the biosynthesis and deposition of the polysaccharides that, once secreted, will become the fungal ECM. Light microscopy will be used for observation of ECM deposition and immunohistochemistry will be used for in situ detection of wall polymers from the fungus using an in-house collection of carbohydrate-binding modules (CBMs)..

    Techniques learnt

    Supervisors
    Dr Alan Little and Assoc Prof Matthew Tucker
    Dr Alan LittleAssociate Professor Matthew Tucker
Adelaide Glycomics
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THE UNIVERSITY OF ADELAIDE
Agriculture, Food & Wine-East building,
Hartley Grove, Waite Campus

Contact

T: +61 8 8313 1284
Email:glycomics@adelaide.edu.au

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