Research projects

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Engineering Crops to Extend Growing Seasons

Supervisors: matt.jones@glasgow.ac.uk

Background

Circadian rhythms are internal body clocks that are commonly experienced as the underlying cause of jetlag. Beyond the human experience, circadian clocks have a crucial role in plant biology, where they serve to measure daylength as well as modulating plants’ responses to light and temperature. Circadian timing therefore enables crops to anticipate daily changes in light and temperature, improving productivity.

This PhD project will utilise our understanding of plant circadian photobiology to extend the growing season for coriander. This will build on Dr Jones’ previous research with the goal of enabling the industrial partner (CN Seeds Ltd) to improve its offering of seeds to market.

It is important that the successful candidate be ambitious and be willing to learn a number of state-of-the-art approaches in plant molecular biology, plant physiology, and in vivo imaging.

Training

The student will join a well-funded research team and be provided training in molecular biology techniques, plant physiology, bioinformatics, and genome editing. The University of Glasgow also offers extensive transferable skills training and core skills training.

•  Further information at Jones Lab

Enquiries

Informal enquiries are encouraged to Dr Matt Jones (matt.jones@glasgow.ac.uk).

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Enhancing Plants’ Responses to Environmental Stress

Supervisors: matt.jones@glasgow.ac.uk, eirini.kaiserli@glasgow.ac.uk

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 confocal microscopy 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. Phytochromes are red photoreceptors that also contribute to temperature sensing. Both phytochromes and the circadian system are well understood, but it remains unclear how phytochromes interact with the clock to coordinate responses to environmental change. During this project we will utilize a constitutively active form of phytochrome to examine how red light and temperature signals are perceived and integrated into the circadian oscillator.

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Chromatin dynamics regulating light and temperature signalling in Arabidopsis

Supervisor: eirini.kaiserli@glasgow.ac.uk

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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CO2 perception and responses in plants – building new connections

Supervisor: Dr Rucha Karnik 

Project summary

Land plants must constantly adjust and adapt to their environment. Environmental fluctuations often culminate in stress for plant growth, disrupt carbon and water balance, and affect crop productivity and fresh-water use. For example, elevated carbon dioxide concentration in air is a major consequence of global climate change. Increasing atmospheric CO2 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 through microscopic pores called ‘stomata’ for photosynthesis and carbon fixation.

Plants respond to increases in CO2 concentration in the air by adjusting stomatal movements and over longer times by altering stomatal density and patterning on the leaf surface. How the perception of elevated CO2 signals connects stomatal movements and long-term development remains poorly understood.

Two PhD positions (Plant Science) are available to work on:

• Project 1. Elucidating aspects of how membrane traffic affects physiology and developmental programmes in plant stomata.
• Project 2. Research to pursue carry physiological and structure function analysis of membrane trafficking proteins using modern proteomics and structural approaches.

The PhD studies will be parts of a larger cross-disciplinary project to understand mechanisms of CO2-regulated membrane trafficking and its impact on plant growth with collaborating partners. It stems from need to address fundamental questions in stomatal biology which will generate advanced platforms for future crop-improvement strategies. Knowledge gained will enhance our understanding of the impacts of global warming and elevated CO2 on land plants in the 21st century.

Successful candidates will work with a team of scientists will have opportunities to gain expertise in molecular cell biology, plant physiology and membrane biochemistry. The students will also develop new experimental set-ups to address fundamental unknowns. Working in 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. Karnik, R. et al. Trends Plant Science 22, (2017)
2. Klejchova, M et al. Plant Physiology 185, (2021)
3. Lawson, T. et al. Plant Physiology 164, (2014)
4. Jezek, M. et al. Plant Physiology 174, (2017)
5. Xia, L. et al. Plant Physiology 180, (2019)
6. Eisenach, C. et al. Plant Journal 69, (2012)
7. Papanatsiou, M. et al. Science 363, (2019)
8. Zhang, J. et al. Current Biology 28, (2018)
9. Lawson, T. New Phytologist 181, (2009)
10. Grefen, C. et al. Nature Plants 1, (2015)
11. Waghmare, S. et al. Plant Physiology 178, (2018)
12. Waghmare, S. et al. Plant Physiology 181, (2019)
13. Karnik R. et al. Plant Cell 27, (2015)

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Profiling Differential Regulation of Proton Transport in Plants for Growth, Nutrition and Immunity project

Project summary

Plant growth and morphogenesis are responsive to environmental stimuli, eg. light, nutrient supply, gravity or pathogen infection. These plant responses are mediated by a complex cascade of signalling events, often driven by plant hormones. Plasma membrane H+-ATPases are primary transporters in plants. These proton pumps are functionally regulated by the plant phytohormone auxin. Activation of the proton pumping energises membrane transport, drives 'acid growth'. The functional regulation of the proton pump activity is a key factor in responses of the plants to their environment including tropic growth and stomatal aperture modulation. Auxin regulates proton pumping at transcriptional and post-translational levels.

Even today, not much is understood about the mechanisms underlying pump traffic and the spatial regulation of proton transport modulators. Plant pathogen are known to manipulate proton pump activity to affect stomatal opening to facilitate infection. Role of membrane traffic in such regulation is not well understood. The findings will open new avenues for future research into mechanisms of plant defence and morphogenesis and will be applied to crop plants for achieving enhanced productivity.

Project aims

• To investigate the mechanistic aspects of differential regulation of the plant plasma membrane proton pumps during infection.
• To study how plant immune responses affect plant growth and nutrition. 

Techniques to be used

Techniques in cell biology, proteomics, biochemistry and plant physiology will be used  using Arabidopsis thaliana as model plants. 

Relevant papers

1. Karnik et al., Trends in Plant Science, 2017 doi:10.1016/j.tplants.2016.10.006
2. Elmore et al., Molecular Plant, 2011 doi:10.1093/mp/ssq083
3. Kundal et al., Plant Cell 2017 doi:10.1105/tpc.17.00070
4. Grefen et al., Nature Plants 2015 doi: 10.1038/nplants.2015.108

Application

• How to apply for a research degree
• For informal inquiries about the project email Dr Rucha Karnik

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Molecular mechanics of clustering and gating in plant ion channels

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

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

Contact:

Michael.Blatt@glasgow.ac.uk

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Photoregulation of plant hormone trafficking and signalling

Outline & aim

The phytohormone auxin (indole acetic acid) is instrumental for directing and shaping plant growth and form. Understanding how this chemical growth regulator controls plant development will have important implications for manipulating plant growth for agronomic gain. Auxin trafficking is profoundly influenced by many abiotic factors, including light. For instance, phototropin receptor kinases (phot1 and phot2) function to redirect auxin fluxes that are required to reorientate plant growth toward or away from light. The phot1-interacting protein Non-Phototropic Hypocotyl 3 (NPH3) is essential for establishing these light-driven auxin movements. However, the mode of action of NPH3 and how it functions to regulate transporter activity remains poorly understood.

This project aims to spatially dissect the site(s) of NPH3 action and how it impacts the subcellular trafficking and function of known auxin transporter proteins implicated in phototropism. Work is also focussed on characterising a newly identified NPH3 protein (NPH3-like, NPH3L) that interacts directly with phot1. Functional characterisation of NPH3, NPH3L and its homologues will provide new insights into the photoregulation of auxin trafficking and signalling associated with phototropism and other phototropin-mediated responses.

Techniques

This proposal is focused on characterising the molecular processes that integrate light and phytohormone signalling, two important agronomic processes associated with manipulating plant growth and optimising photosynthetic efficiency. Both these research areas fall squarely within the strategic priorities of Food Security, Living with Environmental Change and Crop Science. The project will provide excellent training in a range of techniques associated with molecular biology, cell biology, genetics and biochemistry. Training will also be given in key skills including teaching, project-management and science communication. Additionally, the student will have the opportunity to attend and present their research at the international photobiology meetings e.g. Gordon Research Conference in Photosensory Receptors and Signal Transduction, Galveston, Texas in 2016 (which I will chair).

References

• CHRISTIE, J.M. (2007) Phototropin blue-light receptors. Annu. Rev. Plant Biol. 58, 21-45.
• Sullivan, S., Thomson, C.E., Kaiserli, E. and Christie J.M. (2009) Interaction specificity of Arabidopsis 14-3-3 proteins and phototropin receptor kinases. FEBS Lett. 583, 2187-2193.
• Christie, J.M., Richter, G., Yang, H., Sullivan, S., Thomson, C.E., Lin, J., Tiapiwatanakun, B., Ennis, M. Kaiserli, E., Lee, O.R., Adamec, J., Peer, W.A. and Murphy, A.S. (2011) Phot1 inhibition of ABCB19 primes lateral auxin fluxes in the shoot apex required for phototropism. PLoS Biol., 9(6): e1001076.
• CHRISTIE, J.M. and MURPHY, A.S. (2013) Shoot phototropism in higher plants: New light through old concepts. Am. J. Bot. 100, 35-46.

Contact

John.Christie@glasgow.ac.uk

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Synthetic biology for enhancing crop water use efficiency

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

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

Contact

Michael.Blatt@glasgow.ac.uk

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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 a PhD research programme. If not, you will receive the 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