PhD & PD

2014 PhD Research Projects


A          Mechanisms underpinning nutrient foraging by roots

Plant growth and productivity is limited by root growth: its extent and pattern determine its capacity to acquire resources from the soil.  Many essential resources in the soil are immobile and heterogeneously distributed, such as phosphate, iron or manganese; but others are mobile and more homogeneously spread, such as nitrate, ammonium and potassium.  To acquire nutrients they require, plants must therefore continuously optimise two opposing root growth strategies: deep growth to tap into water and water-soluble mobile nutrient pools, and growth of a shallow, highly branched network to acquire heterogeneously distributed resources.  We hypothesise that plants evolved mechanisms to balance costs (carbon and amino acids from the shoot) and benefits (acquisition of limiting, immobile nutrient resources) to control root growth in individual meristems of this highly-branched network.  This project will focus on dissecting the mechanisms underpinning nutrient foraging by roots. The focus will be on how availability of a key limiting nutrient, phosphate results in very diverse root system architecture.

Phosphate stands out as the most heterogeneously distributed macro-nutrient that plants require.  The specific aim of this project is to describe and characterise mechanisms underpinning plant foraging behaviour for phosphate.

Phosphate is the only plant macro-nutrient, which cannot be synthesized (such as nitrogen fertilizers) or obtained from large deposits (such as potash).  ‘Cheap’ phosphate is expected to run out in the next 20-30 years, for food security it is therefore critical to improve crop phosphate use efficiency.

Recent work in our lab has uncovered the mechanisms underpinning control of primary root growth in environments with different phosphate availability in good detail.  The challenge is now to understand the mechanisms underpinning differential growth behaviour of lateral and primary root meristems in these conditions.  The approaches taken in this project will centre on molecular genetics, cell biology (confocal microscopy), image analysis, plant physiology, large-scale data generation and analysis and provide good training in these areas.


B          Exploiting natural mechanisms to control plant growth

Project description:

Plants are constantly exposed to abiotic stress, which inevitably produce large amounts of highly-reactive radicals.  Several thousand DNA damage events occur per cell every hour.  As a result, DNA integrity is constantly threatened.  Plants have evolved mechanisms to protect their stem cells in meristems from such DNA damage, with growth and cell division arrest a key feature of these protective mechanisms.  It is not widely appreciated to which degree plant growth is inhibited by DNA damage, and hence this can be a major limitation to plant productivity.  We have identified novel and entirely unexpected roles for known cell cycle regulators (cyclin-dependent protein kinases [CDK], cyclins and CDK inhibitors) in the DNA damage response.  However, the mechanisms by which these reduce growth and proliferation are still unknown.

While reduced growth capacity is an undesirable trait in good conditions, it is a desirable trait in conditions of abiotic stress (such as drought, excess heat or cold).  This is because reduced growth magnitude diminishes the consequences of abiotic stress and increases the likelihood that the plant survives.

The specific aims of the project are: to characterise the mechanisms of growth arrest during stress-induced DNA damage and the development of synthetic biology modules derived from these natural mechanisms to control growth activity.

Recent work by our group and other labs have started to uncover a complex network of transcriptional and post-transcriptional regulatory mechanisms that orchestrate the plant’s response to DNA damage.  A crucial early step in the signalling pathway is the phosphorylation of the SOG1 transcription factor by the ATM and ATR protein kinases.  This event functions as a switch, and one aspect of the project is to investigate the mechanistic aspects of this switch-like behaviour.  A detailed understanding of this process will then inform the synthetic biology approaches aimed at inducible growth control.

The approaches taken in this project will centre on molecular genetics, cell biology (confocal microscopy), protein biochemistry and synthetic biology and provide good training in these areas.



C          Epigenetic regulation of plant cell differentiation

Cell differentiation is a major event in the life of a cell: when it is generated in a root meristem its identity is defined by its neighborhood, this identity is then fixed when cells become quiescent as they exit the meristem.  Differentiation is essential for a cell to fulfill its function in metabolism, but can be reversed during regeneration.  The transition from a proliferative state to a quiescent state marks the meristem boundary, which is very sensitive to environmental and developmental cues.  For example, abiotic stress will reduce the size of the meristem, and cells will transit to a differentiated state after fewer rounds of cell division.  This project concerns the mechanisms involved in maintaining differentiation in different cell types.  Recent work has implied the involvement of endoreplication – the process by which the genome is replicated in the absence of mitosis – and epigenetic mechanisms in fixing the specific differentiated state. 

The specific aim of the project is: to identify the mechanisms involved in maintaining a specific differentiated state.

Recent work by our group and other labs have started to uncover that the regulatory pathways involved in lateral root initiation are activated as cells are removed from their context in the tissue that maintains their identity.  We have also begun to generate tools to characterise cell state in individual cells or very small cell populations.  Using novel tools, such as microfluidics, the project is to study the dynamic changes to cell identity as cells transit through the meristem or as they are removed from tissues

The approaches taken in this project will centre on molecular genetics, cell biology (confocal, possibly super-resolution microscopy), and synthetic biology and provide good training in these areas.