Research projects

All self-funded projects can be applied to throughout the year. Please note that not all projects are available in the IPhD route. 

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Chromatin dynamics regulating light and temperature signalling in Arabidopsis

Supervisor: Eirini Kaiserli

Outline & aim: Environmental and endogenous stimuli shape plant development, growth and photoprotection by triggering nuclear processes that lead to major changes in gene expression.

This project will focus on understanding how light and ambient temperature signals integrate at the level of transcription to control plant adaptation. The student will characterise the role of novel transcriptional regulators in mediating photo- and thermo-morphogenesis using a series of molecular, cellular, and phenotypic analysis.

Techniques: Confocal microscopy, qRT-PCR, Western blot, ChIP, Next Generation Sequencing (RNAseq, ChIPseq), protein-protein interaction studies, hypocotyl elongation, flowering initiation assays.

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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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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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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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Integrated PhD (October-April)

Our Integrated PhD combines an MSc and PhD project in a 1+3+1 format. There are two options when choosing to apply for the IPhD and these are shown below. Please review how to apply section for more information. 

Option A: Choose from the listed projects.

You can select from the listed projects below and choose your MSc from the options listed on that project. 

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Engineering stomatal patterning in plants for enhanced water use efficiency (available as IPhD)

Supervisor: Rucha Karnik

MSc choices: Food Security [MSc], Biotechnology [MSc]

Outline: Globally, agricultural fresh-water usage has increased 6-fold in the past 100 years, twice as fast as the human population, and is expected to double again before 2030, driven mainly by agriculture. Plant water use efficiency (WUE), defined as the amount of dry matter produced per unit of water transpired is directly related to stomatal function. Stomata of plants are mouth-shaped gates that have the ability to open and close. Stomata facilitate gas exchange, most importantly of water vapour and CO2, between the interior of the leaf and the atmosphere (Jezek and Blatt, 2017). Stomatal behaviours, including movement, density and patterning impacts plant productivity against water use. Thus, stomata represent an important target for breeders interested in manipulating crop performance.

Stomatal development traits, evolved over generations and across species of plants, dictate the distribution and density of the stomata and influence their function (Papanatsiou et al., 2017). For example, the Begonia species of plants display distinct stomatal clustering patterns, an adaptation that facilitates reduced water loss for growth (Rudall et al., 2018, Papanatsiou et al., 2017). Begonias are evolved to grow in tropical montane forests and adapted to a diverse environment. Stomatal patterning in Begonias is thought to have developed as a result of a series of asymmetric divisions opposed to the more common spaced-out single stomata patterns, producing unusual stomatal meristemoids (Tang et al., 2002). In Arabidopsis, a model plant with spaced out stomata, several genes that associate with stomatal development are identified. Yet very little is understood about stomatal patterning and its impact on stomatal function. This project will build upon ongoing work in the lab to resolve the molecular mechanisms driving stomatal clustering using Begonias and to implement this knowledge to engineer stomatal patterns for enhanced water use efficiency in Arabidopsis thaliana model.

The leading theme for the project will be to track variation in stomatal patterning across Begonias in correlation with environment and lineages which are labile and stable, thus revealing the various physiological roles for this unusual feature. This work will be carried out in collaboration with Dr Catherine Kidner, at the University of Edinburgh and the Royal Botanical Gardens Edinburgh that hold genetically verified Begonias. Experimental approaches in molecular and cell biology and stomatal physiology will be employed.

References

1. N. Zoulias, E. L. Harrison, S. A. Casson, J. E. Gray, Molecular control of stomatal development. Biochem J 475, 441-454 (2018).
2. M. Papanatsiou, A. Amtmann, M. R. Blatt, Stomatal clustering in Begonia associates with the kinetics of leaf gaseous exchange and influences water use efficiency. J Exp Bot 68, 2309-2315 (2017).
3. P. J. Rudall, A. C. M. Julier, C. A. Kidner, Ultrastructure and development of non-contiguous stomatal clusters and helicocytic patterning in Begonia. Annals of botany 122, 767-776 (2018).
4. H. Y. X. TANG Min, LIN Jin Xing, JIN Xiao Bai, Developmental Mechanism and Distribution Pattern of Stomatal Clusters in Begonia peltatifolia. J Integr Plant Biol 44, 384-390 (2002).

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Enhancing Plants’ Responses to Environmental Stress (available as IPhD)

Supervisors: Matt Jones, Rea Laila Antoniou Kourounioti

MSc choices: Food Security, Biotechnology, Bioinformatics

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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Examining novel CO2-sensing mechanisms in plants to improve water use efficiency (available as IPhD)

Supervisor: Rucha Karnik

MSc choices: Food Security [MSc], Biotechnology [MSc]

Outline: Elevated carbon dioxide concentration in air is a major consequence of global climate change. Atmospheric CO2 concentration is predicted to rise from pre-industrial level of 280 μmol mol-1, approaching 900 μmol mol-1 by the end of the 21st century. Plants assimilate CO2 for photosynthesis through microscopic pores called ‘stomata’ in exchange for transpirational water loss. The regulation of stomatal density and movements in response to the environment dictates carbon and water cycles on the Earth. Stomatal regulation is sensitive to CO2; for example, plants respond to elevated CO2 rapidly by adjusting stomatal movements, and by long-term changes in stomatal density and patterning on the leaf surface (Jezek and Blatt, 2017).
Experiments will involve the use of model plant Arabidopsis thaliana.

Techniques in cell biology, membrane biochemistry, yeast-based protein-protein interaction studies (Karnik and Blatt, 2023) will be employed. Physiological analysis will include analysis of stomatal physiology, gas exchange, biomass gain and water use. Working withing the vibrant multi-disciplinary research environment at the University of Glasgow, successful candidates will be able to avail personal and career development opportunities to build a career in plant science.

References

1. Jezek, M., and Blatt, M.R. (2017). The Membrane Transport System of the Guard Cell and Its Integration for Stomatal Dynamics. Plant Physiol 174, 487-519.
2. Karnik, R., and Blatt, M.R. (2023). Analyzing Protein-Protein Interactions Using the Split-Ubiquitin System. Methods Mol Biol 2690, 23-36.
3. Xia, L., Mar Marques-Bueno, M., Bruce, C.G., and Karnik, R. (2019). Unusual Roles of Secretory SNARE SYP132 in Plasma Membrane H(+)-ATPase Traffic and Vegetative Plant Growth. Plant Physiol 180, 837-858.

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Mechanics of multifactorial stress responses in plants – How do abiotic stress signals integrate with pathogen immunity? (available as IPhD)

Supervisor: Rucha Karnik

MSc choices: Food Security [MSc], Biotechnology [MSc]

Outline: Plants have the innate ability to respond to pathogens together with multiple abiotic stress challenges, but such responses often come at a cost to plant productivity and water use. Almost 15% of crop produce worldwide is lost to pathogen diseases annually (FAO, 2015). Making the situation worse, climate challenges are predicted to promote drought occurrences, increase soil salinity, elevate global temperature and pathogen loads worldwide (Dai, 2013). The combined challenges of pathogens and abiotic stress are thought to limit agricultural outputs to 30% of the genetic potential. In the face of growing global demand and ever more limited land and water resources, these loses are unsustainable. Hence, resolving mechanistic framework for pathogen and abiotic stress interactions in plants poses a fundamental challenge with relevance for mitigating crop losses.

Stomata are microscopic pores that facilitate the passage of gases and water vapour between the atmosphere and the interior of the leaf across the impermeable cuticle of leaves and stems. Stomatal opening and closing are regulated by environmental factors; for instance stomata open in response to light and the demand for CO2 within the leaf for photosynthesis. Stomata close in the dark, when atmospheric relative humidity decreases, to defend against pathogen entry and to prevent dehydration for plant survival under drought (Jezek and Blatt, 2017). Research in Karnik lab has identified that phytohormone-regulation of plasma membrane H+-ATPase trafficking impacts directly on plant growth, stomatal function and pathogen immunity (Baena et al., 2022, Xia et al., 2020, Xia et al., 2019).

This project builds upon our recent work and will examine mechanisms of plasma membrane H+-ATPase regulation that integrate abiotic stress signals with pathogen immunity. The studies will rely on the extensive knowledge into transport, its kinetics, and its regulation by vesicle traffic (Jezek and Blatt, 2017, Xia et al., 2019), references therein] which has made the guard cell one of the best-known plant cell models, and a promising target for crop engineering (Papanatsiou et al., 2019).
Experiments will be carried out using model plant Arabidopsis thaliana and bacterial pathogens Pseudomonas syringae PstDC3000 to study disease immunity.

Techniques in cell biology, membrane biochemistry, yeast-based protein-protein interaction studies (Karnik and Blatt, 2023) and plant physiology will be employed. Working withing the vibrant multi-disciplinary research environment at the University of Glasgow, successful candidates will be able to avail personal and career development opportunities to build a career in plant science.

References

1. Baena, G., Xia, L., Waghmare, S., and Karnik, R. (2022). SNARE SYP132 mediates divergent traffic of plasma membrane H+-ATPase AHA1 and antimicrobial PR1 during bacterial pathogenesis. Plant Physiol 189, 1639-1661.
2. Dai, A. (2013). Increasing drought under global warming in observations and models. Nature Climate Change 3, 52-58.
3. FAO (2015). Keeping Plant Pests and Diseases at Bay: Experts Focus on Global Measures.
4. Jezek, M., and Blatt, M.R. (2017). The Membrane Transport System of the Guard Cell and Its Integration for Stomatal Dynamics. Plant Physiol 174, 487-519.
5. Karnik, R., and Blatt, M.R. (2023). Analyzing Protein-Protein Interactions Using the Split-Ubiquitin System. Methods Mol Biol 2690, 23-36.
6. Papanatsiou, M., Petersen, J., Henderson, L., Wang, Y., Christie, J.M., and Blatt, M.R. (2019). Optogenetic manipulation of stomatal kinetics improves carbon assimilation, water use, and growth. Science 363, 1456-1459.
7. Xia, L., Mar Marques-Bueno, M., Bruce, C.G., and Karnik, R. (2019). Unusual Roles of Secretory SNARE SYP132 in Plasma Membrane H(+)-ATPase Traffic and Vegetative Plant Growth. Plant Physiol 180, 837-858.
8. Xia, L., Mar Marques-Bueno, M., and Karnik, R. (2020). Trafficking SNARE SYP132 Partakes in Auxin-Associated Root Growth. Plant Physiol 182, 1836-1840.

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Option B: Create your own research proposal

You can create your own project, source a supervisor and they will choose an MSc programme that aligns with your research proposal. 

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Create your own PhD proposal

1. Create your own proposal - approximately 1000 words and must include:
   • a straightforward, descriptive, and informative title
   • the question that your research will address
   • an account of why this question is important and worth investigating
   • an assessment of how your own research will engage with recent research in the field
   • a brief account of the methodology and approach you will take.
2. You will need to contact a supervisor prior to application, using the search function.

Supervisor Search

Based on your proposal, your supervisor will choose an MSc programme that aligns with your research interests. 

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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.

Integrated PhD programmes (5 years)

Our Integrated PhD allows you to combine masters level teaching with your chosen research direction in a 1+3+1 format. 

International students with MSc and PhD scholarships/funding do not have to apply for 2 visas or exit and re-enter the country between programmes. International and UK/EU students may apply.

Year 1

Taught masters level modules are taken alongside students on our masters programmes. Our research-led teaching supports you to fine tune your research ideas and discuss these with potential PhD supervisors. You will gain a valuable introduction to academic topics, research methods, laboratory skills and the critical evaluation of research data. Your grades must meet our requirements in order to gain entry on to your pre-selected PhD research project. If not, you will have the options to pay outstanding MSc fees and complete with masters degree only.

Years 2, 3 and 4

PhD programme with research/lab work, completing an examinable piece of independent research in year 4.

Year 5

Thesis write up.

MSc (Research)

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