University of Dundee

BBSRC EASTBIO Doctoral Training Partnership

BBSRC Eastbio PhD Programme: The role of E3 ligases on the modulation of recombination in cereals

In barley and wheat substantial proportions of the chromosomes are inherited together as a large linkage block, preventing the generation of novel gene combinations and useful variation that could be exploited in breeding and genetics programs. In these crops, the distribution of meiotic crossover events is skewed toward the telomere regions meaning that up to half of the genes rarely if ever recombine.

BBSRC Eastbio PhD Programme: Developing and applying a high - throughput platform in barley to screen for resistance and enhanced susceptibility to aphids

Aphids are economically important pests globally, and can cause significant yield loss of crops, including barley. Currently there are no commercial barley cultivars that are resistant against aphids, and only limited sources of partial resistance have been reported to date. As a consequence, control of aphids mainly relies on the use of insecticides.  In this project we aim to address the lack of available resistance in cereals to aphids pests by identifying new resistance sources in barley.

BBSRC EASTBIO PhD Programme: Molecular characterisation of plant disease resistance genes through novel Next-Generation Sequencing applications

This PhD project will provide comprehensive training for the successful candidate in potato genetics (diploid and tetraploid) as well as plant-pathogen genomics/co-evolution. The student will generate and analyse state-of-the-art Next Generation Sequencing (NGS) data for the genetic mapping and the cloning of resistances effective against the late blight pathogen Phytophthora infestans in established segregating populations.

BBSRC EASTBIO PhD Programme: Tuning the signal – manipulating plant Receptor-like kinases for agronomic gain

Receptor-like kinases are the principal means by which plants perceive their physical extracellular environment. As a result Receptor-like kinases regulate many aspects of development, pathogen perception, interaction with nodulating bacteria and cell wall remodelling and as a result are of particular interest for improving plant responses to environmental perturbations such as climate change and emerging pathogens or improving food yield.

BBSRC EASTBIO PhD Programme: Greasing plant signal transduction – how does reversible S-acylation regulate plant responses to pathogens?

Plants perceive extracellular physical stimuli, such pathogens, symbionts, hormones or cell wall stress, through Receptor-like kinases. Activation of Receptor-like kinases leads to intracellular signalling through multiple routes from the plasma membrane, cytoplasm and nucleus [1]. S-acylation is a lipid based post-translational modification known to regulate many aspects of protein function including affinity for membranes and membrane microdomains.

BBSRC EASTBIO PhD Programme: Novel computational method development for shotgun proteomics

Mass spectrometry (MS) based proteomics is the method of choice for characterizing proteins to understand biological functions and processes, elucidate signalling networks, discover disease biomarkers for human and identify key genes underlying important traits in plants. Computational methods for proteomics play an essential role in interpreting MS data and generating biological insights, but their potentials remains to be fully exploited. Particularly in a plant proteomics experiments, fewer than 20% of the high-quality MS/MS spectra acquired can be meaningfully interpreted.

BBSRC EASTBIO PhD Programme: The link between protein O-GlcNAcylation and intellectual disability

Understanding and controlling the balance between pluripotent self-renewal and differentiation is the major aim of the field of stem cell biology and it is the limiting factor for successful, safe, widespread use of embryonic stem cells (ESCs) in a clinical setting. In recent years it has become clear that these ESC functions are regulated by environmental cues (growth factors, nutrient supply, other cells) via signalling pathways operating on several proteins.

BBSRC EASTIO PhD Programme: The role of autophagy in regulating immunity in the lung

Autophagy is a conserved process that allows cells to break-down and recycle proteins, organelles and remove intracellular pathogens. Although the basic mechanisms are conserved, it is now apparent that in mammalian cells autophagy is subject to complex regulation and can be divided into several distinct forms depending on the target structure. One area in which autophagy regulation is less well understood is in immune cell function. In particular, deregulation of autophagy can have severe consequences for immunological pathologies and, for example, lead to chronic inflammation.

BBSRC EASTBIO PhD Programme: How growth signals regulate replication licensing and cell division in normal and cancerous oesophageal cells

In order to maintain genetic stability and prevent the amplification of chromosome segments, the process of DNA replication occurs in two strictly non-overlapping phases. In late mitosis and G1, DNA is ‘licensed’ for replication by being loaded with double hexamers of MCM2-7 proteins. Then, during S phase, replication forks initiate at these licensed origins. Defects in regulation of the licensing system are associated with a variety of diseases including cancer and growth disorders [1].

BBSRC EASTBIO PhD Programme: Novel anti-bacterial toxins: mode of action and delivery between cells

Many bacterial pathogens use the Type VI secretion system (T6SS) nanomachine to fire toxic ‘effector’ proteins directly into target cells. It is becoming increasingly apparent that the T6SS plays a key role in the virulence and competitiveness of diverse Gram-negative bacteria, including important human pathogens. Pathogens can use T6SSs to directly target eukaryotic organisms, as classical virulence factors. Alternatively, many pathogens can use T6SSs to target other bacterial cells, killing or inhibiting rivals.