PhD applications for October 2025 are now open (see below)

.....If you are interested in applying for a PhD please contact karen.halliday@ed.ac.uk to discuss project options

Lab team work!!

PhD Opportunities - see project descriptions below

We are seeking highly motivated PhD candidates to join our team. If you are interested we are happy to assist with applications for PhD positions, and other types of funding, including scholarships.

LAB Inclusion Statement

Professor Halliday is Dean of Systematic Inclusion and is responsible for overseeing Equality, Diversity and Inclusion (EDI) strategy in the College of Science and Engineering. EDI is very much embedded in lab practice. We celebrate diversity and are proud that our lab team has minority ethnic and white members from different regions of the world and socio-economic backgrounds. Our aim is to provide a welcoming, inclusive environment where everyone can reach their full potential irrespective of background.

You make be interested to watch these short videos tell the stories of Edinburgh PhD students from diverse backgrounds.

Here are some TIPS for studying toward a PhD from Edinburgh students.

Our Research

Molecular signalling: Define the environment-controlled molecular mechanisms that regulate plant growth and development. (molecular-genetics, physiology)

Modelling: Build mathematical models that can predict molecular or physiological biological behaviour. (maths/physics)

Crop development for the future: Develop food crops that can withstand the climate change. (molecular-genetics, physiology)

Social Impact: Working with Social Scientists to challenge discriminatory practices and to evolve an inclusive working environment that attracts and supports diverse employees in STEM.

PhD projects are advertised each Fall, but if you think you would like to join our lab - we strongly encourage you to contact us earlier in the year

Contact: karen.halliday@ed.ac.uk

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Descriptions of PhD projects to start in October 2025

Project 1: Defining the adaptive properties of plant light sensors through synthetic biology and computer vision methods

Primary supervisor, Prof. Karen Halliday; co-supervisors, Prof. Louise Horsfall, Dr Elliot Crowley

Plants are inherently adaptable, a property that is critical for their survival. Their basic structural blueprint is genetically encoded, but their architecture can be modified in response to environmental conditions. In this sense, external cues, such as light, have a profound effect on the way a plant grows and develops, ultimately affecting a plant’s fitness, it’s ability to photosynthesise, and it’s productivity (1).

This project focuses on phytochromes, a unique group of red/far-red light receptors that allow plants to perceive nearby vegetation and elicit adaptive responses, enhancing their ability to compete and thrive in varying environments. It builds on recent technological advances in the Halliday lab, that will bring better, quantitative insights into phytochrome function. The project will develop innovative synthetic tools designed to track changes in phytochrome activity across diverse environments, employing advanced computer vision methods to examine how these shifts in activity affect plant growth. A key component involves creating bioluminescence-based optogenetic constructs that indicate when phytochrome has switched to its "active" state (2). Achieving this will be a major advance, because, as it stands, the detection of active phytochrome relies on cumbersome dual-spectrum spectrophotometric methods that were developed in the 1950s and remain out of reach for many laboratories. The ultimate goal is to understand how phytochrome's photo-sensory properties respond and adapt to the light and temperature conditions found in natural settings. Special emphasis will be placed on exploring phytochrome functionality in green-rich vegetation settings, an area that has not been extensively explored (3).

Training: The project, which will utilise the model species Arabidopsis, will build core expertise in a range of methods that span synthetic, molecular, genetic and AI-based imaging of plant growth. Key components of the project involve developing bioluminescence-based reporter constructs and expressing them in plants through Agrobacterium-mediated transfer. In planta reporter analysis will be conducted through bioluminescence imaging under a range of light/temperature regimes. Complementary molecular-genetic and plant physiological analysis will derive new mechanistic understanding of how phytochrome function changes in differing environments. This interdisciplinary project will gain from specialised knowledge in the Halliday lab (photochemistry, molecular signalling in plants), the Horsfall lab (biotechnology and synthetic methods), and the Crowley group (machine learning and computer vision), which will provide cutting-edge training in biological and AI methods. The programme will provide training in data analysis, hypothesis-based experimentation, critical thinking and report writing.  There will be opportunities to present research at regular lab meetings, at national and at international conferences. The lab also offers career mentoring, and opportunities to gain broader experience in networking, outreach, and diversity and inclusion activities.

References

1. Krahmer J, Ganpudi A, Abbas A, Romanowski A, Halliday KJ. Phytochrome, Carbon Sensing, Metabolism, and Plant Growth Plasticity. Plant Physiol. 2018 Feb;176(2):1039-1048. doi: 10.1104/pp.17.01437. Epub 2017 Dec 18. PMID: 29254984

2. Müller K, Siegel D, Rodriguez Jahnke F, Gerrer K, Wend S, Decker EL, Reski R, Weber W, Zurbriggen MD. A red light-controlled synthetic gene expression switch for plant systems. Mol Biosyst. 2014 Jul;10(7):1679-88. doi: 10.1039/c3mb70579j. Epub 2014 Jan 27. PMID: 24469598

3. Yi C, Gerken U, Tang K, Philipp M, Zurbriggen MD, Köhler J, Möglich A. Plant Phytochrome Interactions Decode Light and Temperature Signals. Plant Cell. 2024 Sep 11:koae249. doi: 10.1093/plcell/koae249. Online ahead of print. PMID: 39259296

Project 2: Building Synthetic Reporting Tools to Study Light Control of Translation

Primary supervisor, Prof. Karen Halliday; second supervisor, Louise Horsfall

This project builds on recent discoveries in the Halliday lab, that significantly expand our understanding of how the phyB light receptor operates under shade conditions. Our unpublished data point to a novel role for phyB in regulating ribosome biogenesis, translation, and plant biomass generation. Collectively, these findings provide a new conceptual framework to understand and interrogate phyB function. 

The project will take a synthetic approach to establishing how phyB regulates ribosome function and translation. A primary focus will be on developing luminescence-tagged constructs to monitor phytochrome levels, activity, and the translation of target mRNAs. Techniques like site-directed nucleotide modification will be utilised to engineer synthetic constructs of the translation machinery. This method offers a means to investigate molecular interactions and assess their functionality. There will also be an opportunity to create translational circuits with improved response to changes in the light environment. Results from this PhD project will be highly relevant for crop research. An expected outcome will be the development of molecular strategies to improve plant biomass production in dense cropping environments (that normally reduce yield).

During the PhD you will benefit from expertise in the Halliday (photochemistry, molecular signalling in plants) and Horsfall (synthetic circuitry) labs, which will provide training in a range of complementary cutting-edge methods. You will acquire a variety of genetic and molecular techniques, such as construct design, BioBrick methods, and agrobacterium-mediated transformation. You will become familiar with methods like translating ribosome affinity purification (TRAP), and assess the effects of modifying translation circuits on plant growth through quantitative 3D plant phenotyping. The programme will provide training in data analysis, hypothesis-based experimentation, critical thinking and report writing.  There will be opportunities to present research at regular lab meetings, at national and at international conferences (online and in-person). In addition, you will be offered career mentoring, and will have opportunities to gain broader experience in networking, outreach, diversity and inclusion activities.

References

Hussain E, Romanowski A, Halliday KJ. PIF7 controls leaf cell proliferation through an AN3 substitution repression mechanism. Proc Natl Acad Sci U S A. 2022 Feb 1;119(5):e2115682119. doi: 10.1073/pnas.2115682119.

Paik I, Yang S, Choi G. Phytochrome regulates translation of mRNA in the cytosol. Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1335-40. doi: 10.1073/pnas.1109683109.

Project 3: Plant Dusk-sensing

Primary supervisor, Prof. Karen Halliday; second supervisor, Dr Lucas Frungillo

Plants are highly malleable organisms, able to continually adjust their growth strategy to a changing environment. This amazing property, known as developmental plasticity, is controlled by a suite of sensor-signalling pathways and the plants internal body-clock. Since plant crowding is common in nature, the ability to detect and adapt to vegetation shade is a critical asset. Indeed, many plants elicit the so-called shade avoidance response as a survival strategy in the face of competition for light resources (e.g. 1).

This PhD will elucidate the molecular mechanism through which shade responses are activated at dusk. Why dusk? During the morning molecular shade avoidance responses are suppressed by the plants biological clock, but later in the day this suppression is lost; we don’t understand how or why (2, 3). This project will solve this problem and will explore the ecological relevance of shade response timing. Additionally, it will examine how temperature, an important environmental factor, influences the molecular response to shade.

Training: The Halliday lab offers a dynamic learning environment with inputs from different disciplines. During the PhD you will work alongside and learn from experts in plant physiology, phenotyping and molecular signalling. An important component of the program will be quantitative analysis of plant growth in different growth regimes. Here you will work with experts in 3D plant imaging to develop skills in image capture and analysis. For the molecular work you will acquire a range of molecular techniques including: DNA/RNA gel electrophoresis, qRT-PCR; protein analysis e.g. western blotting, yeast-two-hybrid, chromatin immuno-precipitation and bioluminescence imaging. The programme will provide training in data analysis, hypothesis-based experimentation, critical thinking and report writing. There will be opportunities to present research at regular lab meetings, at national and at international conferences (online and in-person). The Halliday lab works closely with world-leading scientists in photobiology and other, which will open routes for networking and future collaboration. On joining the lab you will be offered career mentoring, and will have opportunities to gain broader experience in outreach, diversity and inclusion activities.

References

1. Hussain E, Romanowski A, Halliday KJ. PIF7 controls leaf cell proliferation through an AN3 substitution repression mechanism.  Proc Natl Acad Sci U S A. 2022 Feb 1;119(5):e2115682119. doi: 10.1073/pnas.2115682119. PMID: 35086930

2. Salter MG, Franklin KA, Whitelam GC. Gating of the rapid shade-avoidance response by the circadian clock in plants. Nature. 2003 Dec 11;426(6967):680-3. doi: 10.1038/nature02174. PMID: 14668869

3. Martín G, Rovira A, Veciana N, Soy J, Toledo-Ortiz G, Gommers CMM, Boix M, Henriques R, Minguet EG, Alabadí D, Halliday KJ, Leivar P, Monte E. Circadian Waves of Transcriptional Repression Shape PIF-Regulated Photoperiod-Responsive Growth in Arabidopsis. Curr Biol. 2018 Jan 22;28(2):311-318.e5. doi: 10.1016/j.cub.2017.12.021. Epub 2018 Jan 11. PMID: 29337078