Research projects

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Enhancing Plants’ Responses to Environmental Stress 

Supervisors: Matt Jones, Rea Laila Antoniou Kourounioti

Outline & aim: This project will discover how plants integrate light and temperature signals to respond to challenges induced by climate change. The successful applicant will utilize advanced timelapse imaging, next-generation sequencing, and predictive modelling to define the immediate molecular consequences of light and temperature signals.

One crucial component of plants’ sensory network is the circadian clock. In plants these biological timers govern responses to light and temperature (dependent on time of day), whilst also coordinating flowering time. Importantly, the circadian system adapts to prevailing conditions- monitoring circadian readouts consequently provides a robust, integrated measure of environmental responses.

Plants monitor light and temperature changes via a suite of sensory proteins that initiate signaling cascades. During this project we will utilize a combination of engineered photosensors and thermosensors to examine how light and temperature signals are perceived and integrated into the circadian oscillator.

Techniques used:

• Timelapse imaging
• RNAseq
• Mathematical modelling

References:

1. James et al. 2024
   REVEILLE2 thermosensitive splicing: a molecular basis for the integration of nocturnal temperature information by the Arabidopsis circadian clock. https://pubmed.ncbi.nlm.nih.gov/37897048

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Environmental regulation of plant gene expression – the role of ultraviolet light

Supervisor: Gareth Jenkins

Project description: Light is a major environmental factor regulating plant growth and development and has an impact on crop production. Ultraviolet-B radiation in sunlight regulates numerous aspects of plant metabolism, development and physiology (Jenkins, 2017). Many of these responses involve the UV-B photoreceptor UVR8 and entail the regulation of expression of numerous genes (Jenkins, 2017).

The aim of this project will be to understand how the UVR8 photoreceptor is able to regulate gene expression to modify plant responses. Recent research has shown that UVR8 functions by interacting with various proteins, including several transcription factors (Liu & Jenkins, 2024). These interactions alter gene expression and underpin regulatory responses to UV-B. Little is known about these interactions and how they are regulated, but we have recently shown that phosphorylation of UVR8 modifies a specific interaction and alters a key response to UV-B (Liu et al., 2024).

The objectives of the project will focus on particular aspects of UVR8 function and regulation, such as: the molecular basis of interaction between UVR8 and transcription factors; the regulation of UVR8 phosphorylation in plants; the role of phosphorylation in UVR8 action in plant responses to UV-B. The focus of the research will take into account the background and interests of the student.

Techniques: Growth and UV-B treatment of Arabidopsis plants. Protein isolation and immunodetection. Protein interaction assays, e.g. by co-immunoprecipitation. Gene expression assays, e.g. by qRT-PCR. Monitoring plant responses to UV-B e.g. by measuring extension growth and biochemical composition.

References:

1. Jenkins (2017) Photomorphogenic responses to ultraviolet-B light. Plant Cell and Environment 40: 2544-2557.

2. Liu, Giuriani, Havlikova, Li, Lamont, Neugart, Velanis, Petersen, Hoecker, Christie & Jenkins (2024). Phosphorylation of Arabidopsis UVR8 photoreceptor modulates protein interactions and responses to UV-B radiation. Nature Communications, 15: 1221.

3. Liu & Jenkins (2024) Recent advances in UV-B signalling: interaction of proteins with the UVR8 photoreceptor. Journal of Experimental Botany doi: 10.1093/jxb/erae132.

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Light regulation of plant thermoresilience

Supervisor: Dr Eirini Kaiserli

Project description:

High temperatures pose a major threat to plant survival and productivity, and growing evidence suggests that light signalling pathways interact with temperature responses to modulate thermoresilience. This PhD project aims to unravel the molecular mechanisms by which light perception and photoreceptor signalling influence high temperature and heat stress responses in Arabidopsis thaliana.

The project will combine genetics, molecular biology, and cell biology to systematically investigate the light-regulated gene networks and protein complexes that mediate thermotolerance. Using well-characterized photoreceptor mutants, the study will dissect the genetic interactions between light and heat signalling components.

To probe the underlying mechanisms, protein isolation and immunoprecipitation will be employed to identify dynamic protein complexes that form under different light and temperature conditions. Gene expression analysis (qRT-PCR and RNA-seq) will assess transcriptional changes in key regulatory pathways. Confocal imaging will be used to monitor the subcellular localization and dynamics of fluorescently tagged proteins during heat stress under various light regimes. Furthermore, chromatin isolation and chromatin immunoprecipitation (ChIP) will reveal how light influences chromatin accessibility and transcription factor binding during thermal responses.

Complemented by plant phenotyping, this work will provide an integrated view of how light fine-tunes the plant’s ability to cope with high temperatures. Ultimately, the project seeks to identify molecular targets that could be manipulated to enhance crop resilience under climate change.

Techniques: 

• protein isolation
• gene expression
• confocal imaging
• genetics
• plant phenotyping
• chromatin isolation.

References:

• Xu, T., Patitaki, E., Zioutopoulou, A., Kaiserli, E., Light and high temperatures control epigenomic and epitranscriptomic events in Arabidopsis. (2024) Current Opin. Plant Biol., https://doi.org/10.1016/j.pbi.2024.102668

• Quint M, Delker C, Balasubramanian S, Balcerowicz M, Casal JJ, Castroverde CDM, Chen M, Chen X, De Smet I, Fankhauser C, Franklin KA, Halliday KJ, Hayes S, Jiang D, Jung JH, Kaiserli E, Kumar SV, Maag D, Oh E, Park CM, Penfield S, Perrella G, Prat S, Reis RS, Wigge PA, Willige BC, van Zanten M. (2023) 25 Years of thermomorphogenesis research: milestones and perspectives.

• Trends Plant Science, https://doi.org/10.1016/j.tplants.2023.07.001

• RECROP COST, Integrative approaches to enhance reproductive resilience of crops for climate-proof agriculture. Plant Stress, (2025) https://doi.org/10.1016/j.stress.2024.100704

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Molecular mechanics of clustering and gating in plant ion channels

Supervisor: Michael Blatt

Outline & aim: The organisation of ion channels in eukaryotic membranes is intimately connected with their activity, but the mechanics of the connections are, in general, poorly understood. Both in animals and plant, many ion channels assemble in discrete clusters that localise within the surface of the cell membrane. The clustering of the GORK channel — responsible for potassium efflux for stomatal regulation in the model plant Arabidopsis — is intimately connected with its gating by extracellular K+. Recent work from this laboratory yielded new insights into the processes linking K+ binding within the GORK channel pore to clustering of the channel proteins.

This project will explore the physical structure of GORK that determines its self-interaction as a function of the K+ concentration with the aim of understanding its integration with the well-known mechanics of channel gating.

Techniques: The student will gain expertise in molecular biological methods, and a deep grounding in the concepts of membrane transport, cell biology and physiology. Skills training will include in-depth engagement in molecular biology, protein biochemistry and molecular genetic/protein design, single-cell imaging and fluorescence microscopy, and single-cell recording techniques of electrophysiology using heterologous expression in mammalian cell systems and in plants.

References

1. Lefoulon, et al. (2014) Plant Physiol 166, 950-75
2. Eisenach, et al. (2012) Plant J 69, 241-51
3. Dreyer & Blatt (2009) Trends Plant Sci 14, 383-90

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Synthetic biology for enhancing crop water use efficiency

Supervisor: Michael Blatt

Outline & aim: Stomata are pores that provide for gaseous exchange across the impermeable cuticle of leaves. Stomata exert major controls on the water and photosynthetic carbon cycles of the world and can limit photosynthetic rates by 50% or more when water demand exceeds supply. Guard cells surround the stomatal pore and regulate its aperture. Our deep knowledge of guard cells – much arising from this laboratory – gives real substance to prospects for engineering stomata to improve crop yields under water-limited conditions.

This project will engage the synthetic tools of optobiology with the aim of accelerating stomatal responses to environmental drivers, especially light and water availability, both important for crop production. The project will draw on optobiological switches – notably LOV domain peptides – and will use these to control the gating of key ion channels at the guard cell membrane that are known to drive stomatal movements.

Techniques: The student will gain expertise in synthetic and molecular biological methods, and a deep grounding in the concepts of membrane transport, cell biology and physiology. Skills training will include in-depth engagement in synthetic molecular biology, protein biochemistry and molecular genetic/protein design, single-cell imaging and fluorescence microscopy and analysis. Additional training may include single-cell recording techniques in electrophysiology and membrane transport.

References

1. Wang, et al. (2014) Plant Physiol 164,1593-99
2. Lawson & Blatt (2014) Plant Physiol 164, 1556-70
3. Eisenach, et al. (2012) Plant J 69, 241-51

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The improvement of Brassica crops in the changing climate through UV-B signalling

Supervisor: Wei Liu

Project description:

Food security is an urgent global issue, and nowadays this issue must meet the challenge of climate change. Brassica crops are a major source of food and oil worldwide. The main challenges in Brassica crop production are pests and pathogens, heat and drought stresses.
Ultraviolet-B (UV-B) radiation in sunlight regulates many aspects of plant growth and development through the UV-B photoreceptor UVR8, including metabolism, defence, abiotic stress tolerance and morphogenesis. Many responses to UV-B can be very important in crops. However, there is little research on this topic.

The objectives of this project are 1) to discover how UV-B signalling could regulate the model Brassica crop through UVR8 and 2) to explore how to apply this knowledge to improve the resilience of Brassica crops to the changing climate, aiming to provide solutions to the food security issue.

Techniques: 

The project will provide excellent training in diverse techniques of molecular biology, biochemistry, genetics, gene editing, genotyping and phenotyping.  

References:

• Jenkins (2017) Photomorphogenic responses to ultraviolet-B light. Plant Cell and Environment 40: 2544-2557.
• Liu et al. (2024) Phosphorylation of Arabidopsis UVR8 photoreceptor modulates protein interactions and responses to UV-B radiation. Nature Communications, 15: 1221.
• Liu & Jenkins (2024) Recent advances in UV-B signalling: interaction of proteins with the UVR8 photoreceptor. Journal of Experimental Botany doi: 10.1093/jxb/erae132.

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Understanding how phototropin blue light receptor kinase signal from the plant plasma membrane

Supervisor: John Christie

Project description: The ability to enhance photosynthetic capacity remains a recognised bottleneck to improving plant productivity. Phototropin receptor kinases (phot1 and phot2) play an important role in this regard by coordinating multiple light-capturing processes. These include phototropism, chloroplast accumulation movement, stomatal opening, leaf flattening and positioning all of which influence a plant's photosynthetic competence by improving the efficiency of light capture and regulating gas exchange between leaves and the atmosphere. Modulating these processes offers considerable potential to alter plant growth through changes in photosynthetic performance.

Yet, our understanding of how these autophosphorylating kinases initiate signalling from the plasma membrane (PM) is far from complete. Information on their substrates has been limited by the lack of a means to identify their phosphorylation targets in vitro. Gatekeeper engineering can overcome this limitation. The gatekeeper residue within the kinase domain of phots can be engineered to accommodate non-natural ATP analogues such as N6-benzyl-ATPγS6. This modification enables thiophosphorylation of substrate targets that can be detected using specific antibodies. Using this approach, we have now been able to identify new substrate targets. We are therefore able to offer several projects in this area aimed at further charactering the role of receptor autophosphorylation and kinase signalling in the plant model Arabidopsis.

Techniques: The project will provide excellent training in a range of techniques associated with molecular biology, confocal imaging, genetics, and biochemistry. Training will also be given in key skills including teaching, project-management, and science communication.

References:

1. Christie et al. (2018) Plant Physiol. 176, 1015
2. Hart et al. (2019) PNAS 116, 12550
3. Papanatsiou et al. (2019) Science 363, 1456
4. Schanbel et al. (2018) J Biol Cem 293, 5613
5. Sullivan et al. (2021) Nat Commun 12, 6129
6. Waksman et al. (2023) Plant J 114, 390

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Overview

Plant Science at Glasgow is focused on fostering education and training in research to develop sustainable agriculture in an era of global climate change. Our research is centred on exploring how plants respond to their environment to regulate nutrition, water homeostasis, metabolism and various aspects of plant development. Our goal is to apply the knowledge gained from our research to address key issues affecting food security, crop science and technology. Plant Science at Glasgow adopts a multidisciplinary approach within the School of Molecular Biosciences that covers topics such as plant-environment interactions, cell signalling, cell and membrane biology, protein structure and function, gene regulation, synthetic biology, systems biology and translational biology.

Projects are typically related to basic science and integrate with our existing research themes, while other projects are focused on translational aspects of our research. A variety of multidisciplinary research approaches are applied within this research programme, including biochemistry, molecular biology, molecular genetics, biophysics, structural biology, systems biology, polyomics (genomics, transcriptomics, proteomics, metabolomics), bioinformatics and synthetic biology, as well as cellular imaging of biological functions. Specific areas of interest include:

• control of gene expression
• epigenetics and crop improvement
• temperature sensing
• plant mineral nutrition
• protein structure and function
• responses to salinity and drought
• light regulation of plant growth and development
• UV-B perception and signalling
• nuclear organisation and function
• stomatal function and water use efficiency
• ion channel function and membrane transport
• plant-virus interactions and pest resistance
• protein engineering and application
• synthetic manipulation of plant responses

Our PhD programme provides excellent training in cutting edge technologies that will be applicable to career prospects in both academia and industry. Many of our graduates become postdoctoral research associates while others go on to take up positions within industry either locally (e.g. BioOutsource) or overseas (e.g. BASF). We have strong academic connections with many international collaborators in universities and research institutes. Funds are available through the College of Medical, Veterinary & Life Sciences to allow visits to international laboratories where part of your project can be carried out. This provides an excellent opportunity for networking and increasing your scientific knowledge and skill set.

Study options

PhD

• Duration: 3/4 years full-time; 5 years part-time

Individual research projects are tailored around the expertise of principal investigators.

MSc (Research)

• Duration: 1 year full-time; 2 years part-time