ADP-ribosylation is a fundamental posttranslational modification where ADP-ribose is linked on to target proteins by ADP-ribose transferases and removed by the ADP-ribose hydrolases. Emerging data implicate ADP-ribosylation in maintaining the health of the nervous system; mutations in the genes that encode the enzymes that reverse ADP- ribosylation cause neurodegenerative disease in humans and pharmacological inhibition of the ADP-ribose transferases is therapeutically beneficial in various cellular and animal models of human neurodegenerative diseases such as stroke, Parkinson’s disease and motor neuron disease (reviewed in 1). This suggests that ADP-ribosylation regulates key proteins involved in brain aging, however what these proteins are and how they are regulated by ADP-ribosylation is unknown. To elucidate the proteins and underlying mechanisms that regulate brain aging, the student will use an interdisciplinary approach that combines genetics of the fruit fly with molecular and cellular approaches to determine the role of nuclear ADP-ribosylation in the aging and diseased nervous system of the fly (AIM1) and in human cells (AIM2). At the end of this project the student will have identified novel aspects of ADP- ribosylation in the normal and diseased nervous system.

Background reading 1-6

Gurk L, Rifai O, and *Bonini NM. TDP-43, a protein central to amyotrophic lateral sclerosis, is destabilized by tankyrase-1 and -2. J Cell Sci. 2020 May 14

Gurk, L., Rifai, O. M., and Bonini, N. M. (2019) Poly(ADP-Ribosylation) inAge- Related Neurological Disease, Trends Genet 35, 601-613.

Gurk, L., Mojsilovic-Petrovic, J., Van Deerlin, V. M., Shorter, J., Kalb, R. G., Lee, V. M., Trojanowski, J. Q., Lee, E. B., and Bonini, N. M. (2018) Nuclear poly(ADP- ribose) activity is a therapeutic target in amyotrophic lateral sclerosis, Acta neuropathologica communications 6, 84-95.

Gurk, L., Gomes, E., Guo, L., Mojsilovic-Petrovic, J., Tran, V., Kalb, R. G., Shorter, J., and Bonini, N. M. (2018) Poly(ADP-Ribose) Prevents Pathological Phase Separation of TDP-43 by Promoting Liquid Demixing and Stress Granule Localization, Molecular cell 71, 703- 717 e709.

Gurk, L., Gomes, E., Guo, L., Shorter, J., and Bonini, N. (2018) Poly(ADP-ribose) engages the TDP-43 nuclear-localization sequence to regulate granulo- filamentous aggregation, Biochemistry 57, 6923-6926

[6] McGurk, L., Berson, A., and Bonini, N. M. (2015) Drosophila as an In Vivo Model for Human Neurodegenerative Disease, Genetics 201, 377-402.

Dr Yogesh Kulathu

Ubiquitin signalling, which involves the posttranslational modification (PTM) of proteins with ubiquitin, regulates almost every aspect of eukaryotic biology. This versatility is possible because proteins can be modified with different types of ubiquitin codes resulting in distinct functional outcomes. An indispensable role for ubiquitylation is to serve as a signal for the degradation of misfolded and damaged proteins. In addition to degradation, ubiquitin modifications can serve as distinct signals to facilitate intracellular communication. The cellular machinery therefore has to read the different ubiquitin codes in order to ensure that the appropriate response is produced. Further, these codes have to be erased once the functional outcome is produced, a process carried out by a class of enzymes known as Deubiquitinases. In the lab we study these processes, using a range of techniques including biochemical approaches, proteomics, structural biology and mouse models to elucidate new layers of control in protein degradation.

This research is fundamental to our understanding of cell biology in health, and is important, as failures in protein degradation underly many diseases especially age- related diseases such as Alzheimer’s and Parkinson’s disease.

We are looking for an enthusiastic student to join the group to study how protein degradation is regulated by the ubiquitin system. Your PhD will build upon tools, reagents and models we have recently established in the lab. Working on an independent project, you will have the opportunity to learn and apply different approaches ranging from biochemistry, cell biology, genetic screens and state-of-the-art proteomics methods to understand at the molecular level how aberrant proteins are degraded, the ubiquitin signals involved, how they are decoded and how this process is regulated. This project will provide the opportunity to improve our understanding of one of the most fundamental processes in the cell.

Professor Kim Dale

The Notch signalling pathway is one of the key pathways required for the developing embryo. It is especially important for the process of somitogenesis, the formation of body segments that develop into e.g. the bones and muscle of the skeleton. After receiving a signal from a neighbouring cell, the Notch transmembrane protein is cleaved and the Notch intracellular domain (NICD) is released and translocates to the nucleus where it controls expression of developmental specific gene cohorts.

Recent research in the JKD lab has identified unique residues in NICD that are phosphorylated in presomitic mesoderm (PSM) cells but are not detected in other cell types. Phosphorylation is a key process in the regulation of the stability of NICD. NICD is more unstable in PSM cells compared to other cell types. This is potentially a really important factor as NICD levels oscillate during somitogenesis, with NICD levels changing from high to low to high again in a 5 hour cycle and the regulation NICD stability is critical for this process.

This project will be using human induced pluripotent stem (iPS) cells that will be differentiated into PSM cells. This is an in vitro model system for the human embryo. The lab is currently also developing protocols for the generation of gastruloids, stem cell derived 3D structures that form somite like structures that can be used to determine if these phosphorylated residues are critical for somitogenesis. The main aim of this project is to determine the function of the phosphorylation of the newly identified phosphoresidues in NICD and the factors and mechanism responsible.

Professor Ron Hay

SUMO has diverse roles in cellular physiology that in most cases are mediated by its ability to interact non-covalently with hydrophobic patches of low sequence complexity known as SUMO Interaction Motifs (SIMs). Extensive proteomic analysis has documented the co-ordinate SUMO modification of many components of large nucleo protein complexes. An emerging mode of action of SUMO is that multiple members of large protein complexes, rather than single proteins, are targeted for modification by the limited number of SUMO E3 ligases. Although the modification of components of the complexes may be sub-stoichiometric this still allows them to interact non- covalently with the more abundant SIM sequences. This serves to increase the stability of the complex such that it attains or retains biological activity. In this situation SUMO modification is acting as a relatively unspecific biological glue. The aim of the project is to determine the molecular basis for the recognition of the nucleoprotein complexes and the SUMO modification of their protein components.

Dr Tony Ly

T lymphocytes mediate long-term adaptive immunity to viruses and tumour cells. T lymphocytes recognize foreign antigens via specific interactions with the T cell receptor (TCR) that is expressed on the cell surface. Upon antigen-TCR engagement and appropriate co-stimulation, T lymphocytes undergo major remodelling of the proteome and cellular metabolism, expanding in volume by ~3.5-fold and entering a period of rapid cell division cycles. This proliferation is important to clonally expand the antigen-specific pool of T lymphocytes and clearance of diseased cells. The rapid divisions that characterise T lymphocyte proliferation resemble embryonic cell division cycles, in which gap phases of the cell cycle are shortened. However, the mechanisms that control cell division in T lymphocytes are poorly understood.

In this project, the student will use CRISPR/Cas9 gene deletion and lentiviral overexpression of key cell cycle control factors to investigate their role in T lymphocyte proliferation. The student will receive training on state-of-the-art molecular biology and cell biology techniques, including the culture of murine T lymphocytes, Cas9 genome editing, lentivirus generation, and flow cytometry. The student will be embedded in a dynamic laboratory environment, with regular group meetings with the host lab and joint lab meetings with other research groups, providing ample opportunity for networking and feedback. Interested candidates are highly encouraged to contact the lab head directly for more information ([email protected]).

Meiosis is a specialised type of cell division that produces haploid daughter cells known as gametes that are important for sexual reproduction. Dynamic protein phosphorylation plays crucial roles during meiosis, but the mechanisms underlying the function of each kinase are not entirely clear. Cyclin-dependent kinases (CDKs) are a family of key kinases with different roles during the cell cycle. CDKs are the active kinase component of CDK/cyclin complexes. Several CDK/Cyclin complexes exist and they regulate different stages of the cell cycle. Mammals and other species such as nematodes possess an array of CDKs to carry out a range of cell cycle activities. One member of the family, CDK-1, is highly conserved among eukaryotes and a primary regulator of mitotic progression. Additionally, CDK-1 was found to be essential for embryonic development as well as meiotic oocyte resumption in mice. These results align with a study in the nematode C. elegans where CDK-1 was discovered to be vital for meiotic progression to metaphase I. Despite these results, little is known about the precise roles CDK-1 plays during oocyte meiosis and dissecting the specific roles and timing of CDK-1 kinase activity during meiosis remains an important unanswered question. The use of conventional, chronic deletion/depletion strategies (knockout and RNAi) are not suited to address CDK-1’s roles during chromosome segregation because CDK-1 regulates meiotic events in prophase in mouse and C. elegans oocytes. While the use of the classic CDK-1 inhibitor RO-3306 has given more insight into the requirement for Cdk1 activity during cell division, RO-3306 can inhibit other kinases, such as Cdk2, at fairly low concentrations. Hence, the main question we aim to answer is 1) what are the specific roles of Cdk1 during chromosome segregation in oocytes?

To this end, a means to acutely deplete or inhibit Cdk1. My lab has experience with three complementary methodologies: 1) Auxin-induced degradation (AID); 2) temperature-sensitive (ts) alleles; and 3) analogue-sensitive (as) alleles (a.k.a. chemical genetics). These methods overcome the problems of traditional RNAi-mediated depletion, with AID achieving protein degradation within minutes/hours, fast-acting ts alleles inhibiting function in minutes, and as alleles achieving inhibition virtually instantly. We will then investigate what cyclins are important for each of the functions. All B-type cyclins have non-overlapping functions during oocyte meiosis, but what these functions are remains unknown. Thus, the second question is 2) what are the different cyclins associated with Cdk1 function(s) in oocyte meiosis? 

Professor Tom Owen-Hughes

One of the unanticipated outcomes of population-based genome sequencing has been the finding that genes involved in the regulation of many genes are mutated at high frequency in tissue specific cancers. This is the case for SWI/SNF –related chromatin remodelling enzymes which are mutated in about 20% of all tumours and at higher frequencies in cancers of specific tissues. To understand how these genes function we have engineered cell lines in which specific subunits of these enzymes can be degraded rapidly and specifically. In this project, chromatin immunoprecipitation and RNA sequencing will be used to gain insight into how these complexes function. In the long run characterising these pathways will provide new routes for the development of cancer therapies.

Professor Kim Dale

One of the key processes in embryo development is somitogenesis. This is the formation of segments, known as somites, that go on to develop into bone and skeletal muscle. This process is tightly regulated and it is now known that one of the key signalling pathways in this regulation is that of Notch. After receiving a signal from a neighbouring cell, the Notch transmembrane protein is cleaved and the Notch intracellular domain (NICD) is released and translocates to the nucleus where it can impact the expression of numerous other genes. During somitogenesis the expression of a number of genes oscillate, these are collectively known as clock genes. It is believed that these clock genes are responsible for the regular budding off of new somites during somitgenesis. One of the most studied clock genes is Hes7. It is also known that NICD levels oscillate with the same period as the clock genes.

Pilot data from the JKD lab suggest that in the presomitic mesoderm (PSM – the tissue that differentiates into the somites) levels of NICD present in the nucleus differ across the stages of the cell cycle. A recent publication from another lab has shown that the length of the cell cycle is dependent on where on the Hes oscillation the cell begins mitosis. Given that aberrant Notch signalling has been shown to have a role in many diseases, including certain cancers and developmental disorders, there is clearly a need to elucidate the interaction between Notch signalling and cell cycle dynamics.

This project would use molecular tools currently being generated by the JKD lab to investigate the relationship between the clock gene Hes7, the cell cycle and NICD levels in PSM cells. The main aim would be to look at how the cell cycle effects levels of NICD and what the downstream impact of this is on protein and RNA levels within the PSM. There would also be the potential to explore the mechanism behind this regulation.

Dr Sarah McKim

From the earliest farmers to modern plant breeders, humans have continually modified the body plan of cereals, sometimes drastically, to generate higher grain yields. Excitingly, recent work in the McKim lab suggests that architecture in barley, a key global crop, is controlled by jasmonate, a classic plant stress/defense hormone (Patil et al., 2019). However, we don’t know how other pathways controlling architecture interact with jasmonate or whether environmental cues use jasmonate to control barley development. In this project, the student will use genetic analyses and physiological experiments to understand how the jasmonate pathway controls development in barley. The student will also explore how jasmonate may alter susceptibility to pathogens and pests. Taken together, you will reveal the developmental roles of jasmonate in barley and advance our understanding of interactions which influence stem elongation and flowering.

Students with a passion for research who are motivated by a desire to improve food security are the best fit for this project. The student will also benefit from a unique training environment offered by the Division of Plant Sciences, based at the James Hutton

Institute (JHI), one of the best centres in the world to study cereals, and the site of the new International Barley Hub (2).

Patil et al (2019) APETALA control of internode elongation in barley.Development.146(11).pii:dev170373

https://dev.biologists.org/content/146/11/dev170373

http://www.barleyhub.org/

Professor Simon Arthur

Fungal pathogens represent a significant clinical problem for which treatment options remain limited. While in healthy individuals localised fungal infections are usually cleared by the immune system, systemic or blood stream fungal infections are a serious clinical issue, with mortality rates of 40-50% even with modern treatments. This is being compounded by the emergence of resistance to the limited number of anti-fungal infections. Systemic fungal infections are most common either as a hospital acquired infection or in immunocompromised individuals – such as HIV patients and those on chemotherapy or other immunosuppressive treatments.

While a number of fungal species can cause systemic infection, Candia species, and in particular Candida albicans, are the most common. Despite this we know relatively little about how fungal pathogens affect intracellular signalling in immune cells. Tissue macrophages are one of the cells to respond to pathogens and help coordinate the subsequent immune response in addition to their role in phagocytosing and killing pathogens. The macrophage’s response to Candida is however substantially different to those triggered by bacterial pathogens, however it clear what the critical signalling pathways in the macrophage are following Candida infection. To investigate this, phospho-proteomics will be used to examine how Candida infection affects signalling cascades in macrophages in an unbiased manner. Using the data from the this, networks of activated pathways will be established. The roles of these pathways will then be tested using a combination of small molecule inhibitors and siRNA. The project will therefore allow us to be understand the innate response to Candida and potentially identify targets that could be used to develop drugs to boost the immune response to Candida

Dr Jens Januschke

Posttranslational modifications of proteins are important regulatory events that impact most if not all physiological functions of cells. The lab is interested in how different cell fates are established by stem cells that can divide asymmetrically. This is important to understand as deregulated fate decisions by stem cells are suspected to lead to tumour- like growth.

This project will focus on phosphorylation of proteins in a model system stem cell, the neural stem cells of the fruit fly. You will use state-of-the-art live cell imaging of CrispR generated fluorescent reporters of kinase activity as well as nanobody based reporters to detect specifically the phosphorylated pool of candidate proteins in cells to study their dynamics and manipulated their localization. This project will shed light on our understanding of how the evolutionarily conserved PAR polarity complex drives cell fate decisions

Dr David Murray

Membranes and their protein organization are a frontier in our understanding of cell biology. We focus on polarized trafficking as a model to uncover fundamental mechanisms in the organization of structures at membranes. We aim to understand the role of protein complexes including the exocyst in this pathway. This project seeks to answer mechanistic questions regarding 1) the regulation of protein structural mechanics in polarized trafficking, 2) and the consequences of signalling on this pathway and its organization. Because signalling in polarized trafficking is affected in metastasis of cancer, we position our research for the broadest impact in forming a foundation for drug discovery.

We take a reconstitution and synthetic biology approach in combination with the powerful tools available for microscopy and experimental cell biology, including methods such as stem cell biology and cryo electron microscopy. Our philosophy is to address questions of challenging biology using quantitative methods in a hypothesis-driven approach.

We are excited to introduce this interdisciplinary research to a highly motivated and ambitious student, who will be expected to have exemplary communication skills and an ability to collaborate. The student will emerge a master in state-of-the-art protein and cell biology approaches. For any questions on the nature of the proposed research, please to not hesitate to contact me directly [email protected] or by visiting our website. https://sites.dundee.ac.uk/david-murray-lab/

The selective degradation of the endoplasmic reticulum via autophagy, also known as ERphagy, is a fundamental cellular process that has been observed under different stresses and stimuli. However, the exact rationale and contribution of ERphagy towards cellular homeostasis remains unclear, let alone its clinical implications. Recent emerging data suggest that dysregulation of ERphagy might contribute to neurodevelopmental defects, pancreatic stress, and cancer progression, albeit with unclear mechanisms. This project will aim to compare the autophagy cargo content during different stress induced ERphagy by mass spectrometry. We will then employ CRISPR-based interference and activation approaches (CRISPRi and CRISPRa) to understand the rationale for removing these cargos, and the impact of their failed removal on ER and overall cellular homeostasis.

Dr Piers Hemsley

Plants, being sessile organisms, must sense and respond to environmental change, such as temperature or drought, without being able to move. Evolution has led to a diverse array of detection, signalling and mitigation responses, and understanding how these function and can be manipulated is a crucial factor for maintaining food security in response to climate change.

Osmolarity Induced Ca2+ (OSCA) ion channels are conserved across eukaryotes (TMEM63 family; Murthy et al., 2018. eLife 7:e41844) and are used by plants to detect and respond to changes in osmotic potential. OSCA channels are thought to do this by detecting changes in membrane tension and rigidity (Douget & Honoré. 2019. Cell 179(2): 340-354). However, no mechanism underlying this hypothesised mode of action has been identified. We recently discovered that many OSCA ion channels are subject to a poorly understood type of post-translational modification called S-acylation. S-acylation involves the addition of long chain fatty acids to cysteine residues in proteins and acts to promote interaction of proteins, or domains of proteins, with membranes. S-acylation is unique amongst lipid modifications of proteins in that it is reversible; this allows it to regulate function in a similar way to phosphorylation or ubiquitination. S-acylation would provide an ideal mechanism for OSCA channels to detect changes in membrane tension, rigidity and fluidity. We have since found evidence that OSCA channels are some of the most dynamically S- acylated proteins within the plant cell, indicating that OSCA channel function is regulated at some level by S-acylation.

This project aims to elucidate how S-acylation affects OSCA channels in plants to provide greater insight into how plants mitigate against environmental stress. This will be done using an interdisciplinary approach, combining laboratory-based plant physiology, molecular biology, S-acylation assays, chemical biology, structural biology and biochemistry. You will join a diverse and collaborative lab with opportunities for a wide range of scientific and transferrable skills training. Recent ~£65 million investment in the Advanced Plant Growth Centre and International Barley Hub ensure that cutting edge plant growth facilities are available, in addition to the world leading biochemical, molecular, computational and imaging expertise and facilities at Dundee and Durham.

This work will be a collaboration between the laboratories of Dr Piers Hemsley (Dundee), Prof. Ulrich Zachariae (Dundee) and Prof. Marc Knight (Durham). For further details and informal discussion prospective students are strongly encouraged to contact Dr Piers Hemsley ([email protected]) before submitting an application.

Dr Piers Hemsley

Full title: Targeted protein degradation in plants – developing “Green PROTACs” for functional analysis of lethal genes

Climate change is one of the biggest threats to global food production, leading to unpredictable weather patterns and geographical migration of pathogens. As sessile organisms, plants must respond to a changing environment in situ and have developed complex systems of perception and response to mitigate against environmental stress. Understanding the function of these proteins is crucial to informing breeding and crop development programs to mitigate against climate change, emerging pathogens, food insecurity and fresh water shortage.

Functional studies of plant genes and their proteins is often hampered by lethal phenotypes when genes are mutated or severe mutant phenotypes prevent examination of plant life stages or processes of interest. Historically, these genes have proved almost impossible to study at a functional level. In animal systems the emergence of Proteolysis Targeting Chimeras (PROTACs), that selectively degrade a protein of interest through the artificial recruitment of ubiquitin ligases, has proved to be powerful tool for functional determination. However, PROTACs have not been established in plants. This project aims to bring this powerful technology to the study of plant proteins, enabling otherwise impossible research questions to be addressed. Based on exiting BromoTAG work at Dundee (Bond et al., J. Med. Chem. 2021, 64, 20, 15477–15502) we have synthesised a range of PROTACs that will recruit plant ubiquitin ligases to proteins of interest. The aims of this project are to characterise these PROTACs for the ability to direct degradation of proteins in plants and, where necessary, collaborate with chemists to improve uptake or activity.

This is an interdisciplinary biotechnology project, co-supervised by Prof Alessio Ciulli, primarily providing skills in plant molecular biology, protein biochemistry and plant transformation, but necessitating close working with structural biologists and chemists.

You will join a diverse and collaborative lab with opportunities for a wide range transferrable skills training. Recent ~£65 million investment in the Advanced Plant Growth Centre and International Barley Hub ensure that cutting edge plant growth facilities are available, in addition to the world leading biochemical, molecular, structural, chemical and proteomic expertise and facilities at Dundee. For further details and informal discussion prospective students are strongly encouraged to contact Dr Piers Hemsley ([email protected]) before submitting an application.

Prof Nicola Stanley- Wall

Professor Sarah Coulthurst

Interbacterial competition is ubiquitous and plays a key role in shaping diverse microbial communities, including the gut microbiota and in the rhizosphere. Bacteria normally exist within mixed microbial populations and must be able to compete effectively for space and nutrients to enter and survive within these communities.

Bacillus subtilis is a Gram-positive, spore-forming bacterium that resides in intestinal tracts, soil, and on plant surfaces. B. subtilis, alongside other Bacillus species, presents a promising plant growth–promoting rhizobacteria.  We predict that a clear understanding of B. subtilis intraspecies competition will allow us to better select plant growth-promoting strains that can outcompete existing B. subtilis isolates that already reside in the environment.

Polymorphic toxin systems (PTS) are a hallmark of bacterial competition. These systems can transport toxic proteins with polymorphic C-terminal domains into nearby bacteria. Targeted cells that lack the intracellular cognate antitoxin (immunity) protein are killed or have their growth inhibited. B. subtilis has been found to utilize multiple differing PTS to mediate intraspecies antagonism. The aim of this project is to use molecular biology coupled with bioinformatics and biochemistry to further our understanding of these antagonistic interactions.

Alongside developing your laboratory skills, you will be given training in data management and presentation skills and will be provided ample opportunities to develop other professional skills that you wish to enhance.

Professor Kim Dale

During early embryogenesis, segments (somites) are formed during a process called somitogenesis. These somites will go on to form the bones and muscles of the skeleton. The timing of the segmentation process is regulated by a molecular oscillator, the segmentation clock, that drives cyclic gene expression with a periodicity that matches somite formation. This process is tightly controlled, and dysregulation of the segmentation clock results in diseases such as congenital scoliosis.

For the segmentation clock several levels of regulation of clock gene expression are important: transcriptional activation and negative feedback loops, post transcriptional regulation (from splicing to RNA stability) and protein degradation. m6A modification of mRNAs is critical for many post transcriptional processes. It plays an important role during embryonic development and aberrant m6A modification is linked to several diseases.

This project will investigate how m6A modification controls the segmentation clock and the formation of somites in human induced pluripotent stem cell (hiPSC) derived presomitic mesoderm (PSM) cells as well as in hiPSC derived 3D structures called somitoids. It will provide insights into the mechanisms required for accurate segmentation clock gene expression in embryonic development as well as diseases associated with misregulation of the segmentation clock or the signalling pathways involved such as congenital scoliosis and T-cell acute lymphoblastic leukaemia (T-ALL).

Aims of the project:

Establish the role of m6A modification for the regulation of segmentation clock expression
Identify regulatory elements in clock gene mRNAs and the proteins that regulate these elements
Establish how this impacts the segmentation clock and somitogenesis

Examples of techniques expected to be used during the project: maintenance of hiPSC, CRISPR modification of hiPSC, differentiation of hiPSC into PSM cells, generation of hiPSC derived somitoids, immuno fluorescence, in situ hybridisation, microscopy, purification of DNA, RNA and protein, RT-qPCR, Next Generation Sequencing, immuno precipitation, western blotting, mass spectrometry, analysis of large data sets.

Professor Simon Arthur

Idiopathic pulmonary fibrosis (IPF) is a progressive disease that results in an irreversible decline in lung function. At present IPF is normally fatal and the median survival is between 2 and 5 years after diagnosis. While some drugs, such as Pirfenidone and Nintedanib, can slow progression they do not provide a cure, and so further research is needed in order to increase our understanding of fibrosis and identify novel targets for therapeutic development. Lung fibrosis can be induced by the chemotherapy agent bleomycin, and this can be used as a model for IPF in mice. Bleomycin induced fibrosis is dependent on IL-33, a cytokine released by damaged endothelial cells in the lung. The mechanism by which IL-33 promote fibrosis however remain controversial.

To understand the changes induced by bleomycin in the lung, and how these change on IL-33 blockade, this project will use high resolution mass spectrometry to map changes in protein expression throughout the lung as fibrosis progresses. Initial results will focus on the whole lung tissue. Recent advances in DIA based mass spectrometry mean it will be possible to quantify 6000 to 7000 proteins and identify what changes with disease progression. This will allow quantification of changes in the extracellular matrix and start to identify changes in cellular function. This will be followed by further proteomic experiments on isolated cell types from the lung. Together this will help establish the mechanism behind fibrosis and potentially help identify novel biomarkers or therapeutic targets.

Professor Simon Arthur

Microglia are the major innate immune cells in the central nervous system and are required for the response to invading pathogens, removal of damaged or apoptotic cells and also contributing to neuronal development via synaptic pruning. To achieve these diverse functions, microglia must be able to adopt a spectrum of pro- and anti-inflammatory phenotypes. The balance between the phenotypes is affected by aging, with microglia from older individuals displaying a greater propensity for an inflammatory phenotype. This in turn may promote age-related pathologies in the CNS. The factors which control the polarisation of microglial phenotypes are however not well understood. This project will seek to understand the factors controlling microglial polarisation and how these impact on processes in healthy aging and neurodegeneration.

In the peripheral immune system, macrophages play a similar role to microglia in the CNS. Anti-inflammatory phenotypes in macrophages are regulated by the SIK kinase family, which are in turn regulated downstream of G protein coupled receptors that activate cAMP signalling, such as the prostaglandin E2 (PGE2) receptors EP2 and 4. Multiple isoforms of the PGE2 receptor exist and the effects of PGE2 are dependent on the receptor isoform expressed by the cell; EP2 and EP4 activate cAMP signalling while EP3 inhibits due to differential use of Galpha subunits. In the proposed project we will examine the role that the SIK pathway plays in regulating microglial function downstream of PGE2, which has immunomodulatory effects in the CNS, and adenosine, which has roles in both neurotransmission and immunomodulation as well as potential links to ageing. Similar to PGE2, adenosine acts via receptors that are in the GPCR family, and like PGE2 receptors different adenosine receptor isoforms have differential effects on cAMP signalling. To address which receptor isoform is critical, synthetic agonists or antagonists for specific PGE2 or adenosine receptor isoforms will be used, and differences in isoform expression and utilization in microglia from young and aged mice will be examined. High resolution proteomics using sate of the art mass spectrometry will be used to examine the effects of PGE2 and adenosine on proteome remodelling in microglia, and this will be linked to functional assays to determine the inflammatory phenotype of the cells. Finally to extend the studies into humans, human iPS cell derived microglia will be analysed. Together these approaches will enhance our understanding of how microglial function is controlled during ageing. The project will provide training in a range of techniques including mass spectrometry, bioinformatics and stem cell culture.

Dr Varsha Singh

The ability of bacteria to spread within the organs and tissues of their host underlies their ability to establish successful infection. Certain bacteria such as Gram-negative bacterium Pseudomonas aeruginosa are exceptional at displaying various forms of motility. Under specific conditions, a group of P. aeruginosa cells can move together under the influence of quorum sensing and biosurfactant, using a process called swarming. Swarming bacteria have been shown to be resistant to antibiotics. We aim to understand the environmental triggers of swarming so that the spread of bacteria could be controlled. In our previous work, we have shown that ethanol produced by microbes is a trigger for swarming (Badal et al. mBio 2021) and iron limitation promotes rhamnolipid production (Pradhan et al. BiorXiv 2022). To identify components of the core machinery that regulates swarming in P. aeruginosa, we screened 5800 mutants of the bacterium and identified 271 genes to be essential for swarming. The Master's project is focused on finding if other neighbours of P> aeruginosa inhibit or promote swarming. We will utilize other lung resident pathogens such as Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii and Cryptococcus neoformans.

The student will learn to study these pathogens safely. S/he will utilize a GFP reporter for rhamnolipid, surfactant quantification assays as well as qRT-PCR for ascertaining the effect of neighbours on Rhamnolipid production and plate based assays to quantify swarming itself. The ability of neighbours on swimming and quorum sensing in P. aeruginosa will be assessed using reporters for flagella and for autoinducer production.

During the course of the project, you will learn some molecular biology techniques and various assays for P. aeruginosa including swarming and swimming, molecular biology and imaging of bacterial cells. You will be mentored on various components of research including hypothesis generation, execution, analysis of data and interpretation, manuscript writing etc.  

Relevant references from the Singh Lab:

Pradhan, D., Tanwar, A., Parthsarathy, S. and Singh, V. Toroidal displacement of Klebsiella pneumoniae by Pseudomonas aeruginosa is a unique mechanism to avoid competition for iron. bioRxiv (preprint) https://doi.org/10.1101/2022.09.21.508880

Badal, D., Jayarani, A.V., Kollaran, M.A., Prakash, D., Monisha P., Singh, V. Foraging signals promote swarming in starving Pseudomonas aeruginosa. mBio 2021, 12(5):02033-21.

Kollaran, M.A., Joge, S., Harshitha, K., Badal, D., Prakash, D., Mishra, A., Varma, M.M. and Singh, V. Context-Specific Requirement of Forty-Four Two-Component Loci in Pseudomonas aeruginosa Swarming. iScience. 2019 13: 305-317.

Dr Varsha Singh

Animals rely on their sensory system to find food and avoid predators. Although olfaction and gustation have been well studied, effect of mechanosensation on food search is underexplored although touch is used frequently in human infants. WE propose to use a model animal to study this.

Caenorhabditis elegans is a bacterivorous nematode. The genetic tractability, short developmental phase of 2-3 days, and optically transparent soma of 1 mm length make it a very useful model for studying the development of sensory systems for touch, taste and odours. In our ongoing work, we have found that chemosensory function is gained late in larval development. We hypothesize that the mechanosensory system develops early in the development of worms and larvae use touch modality (texture of food bacteria, mucoidy) to find food. Specifically, we hypothesize that PVD neurons with dendrites underlying the entire body wall, develop early during development and assist in mechanosensation-based food search. In this project, we will use an imaging-based approach to study the formation of the dendritic arbour of GFP expressing PVD neuron in larval stages L1, L2, L3 and L4. We will also perform functional mechanosensation analysis (touch response) in all 4 larval stages. Finally, we will study the food choice behaviour of all 4 larval stages when bacteria with differing textures (Escherichia coli, nonpathogenic Pseudomonas aeruginosa and Enterococcus faecalis) are presented as food choices.

As part of this project, you will learn C. elegans maintenance, touch response assays, food choice assays and fluorescence microscopy. You will be mentored on various components of research including hypothesis generation, execution, analysis of data and interpretation, manuscript writing etc.  

Relevant references:

Dr Liz Miller

Roughly one third of the human genome encodes secretory and membrane proteins. Following synthesis in the endoplasmic reticulum (ER), these proteins are captured into transport vesicles for delivery within the cell. ER export receptors play critical roles in deciding which proteins get trafficked, yet we know relatively little about the mechanisms by which these recognition events occur.

This project aims to examine the full spectrum of secretory proteins that use different export receptors in different immune cells. By making genetically modified T- and B-cells, we aim to differentiate cells into different effector cell types and use proteomics to understand (i) the full spectrum of proteins secreted by different specialized cells; (ii) the impact of knock-out or knock-down of specific secretion machineries on the secretome landscape; and (iii) the mechanisms that different export receptors use to engage diverse cargo clients.

The project will allow a student to develop skills in a variety of biochemical and cell biological approaches, including genome editing, cell culture, proteomics, biochemistry and live-cell imaging. Both the Miller and Howden labs are small groups, focused on questions central to this project, and provides a supportive mentoring environment.

Dr Hajk-Georg Drost

Drug discovery is the systematic process of identifying and optimizing molecular compounds to develop targeted medications for medical conditions. While proven hugely successful in the past decades, conventional methodologies are often limited by extensive timelines, elevated costs, and alarmingly high failure rates. This project seeks to navigate through these challenges by exploring how the comprehensive power of comparative genomics and artificial intelligence can be leveraged when catalysed by the diversity of billions of proteins across the Tree of Life.

This computational biology project centres around three pivotal objectives. Firstly, it seeks to identify novel drug targets by comparing the genomics of a myriad of biodiverse organisms to uncover evolutionary conserved or divergent molecular pathways with therapeutic potential. Secondly, it aims to discover bioactive compounds by probing through the genomes of various species to spotlight novel protein variants with prospective applications in human medicine. Lastly, the project seeks to prototype predictive models for drug efficacy and safety testing by quantifying the genetic variability found across different species and assessing their predictive power when employed to a more constrained variability known to exist in human populations.

For this purpose, the appointed candidate will gain early access to our clustered protein universe, comprising 1.7 billion clusters derived from a vast 20 billion protein sequences spanning all sequenced species or strains across the Tree of Life (Buchfink et al., 2023). These protein sequences, processed using our search engine DIAMOND2 (Buchfink et al., 2021), each possess a taxonomic label (including 'unknown'). This comparative genomics approach will allow us to associate well-established molecular compounds such as ubiquitination pathways or ubiquitin-like protein families with the protein biodiversity found across a diverse range of species and microbial strains across the Tree of Life.

We anticipate that this project will streamline early efforts to establish a comprehensive database of potential drug targets and bioactive compounds derived from the diversity of the protein universe across the Tree of Life. Such a database will facilitate further efforts to leverage the conservation and divergence of specific biological pathways and mechanisms across species for predictive models of therapeutic potential.

While crafted for a Master's program, this project aspires to shed light on underexplored biological pathways, unveiling putative novel drug targets and therapeutics, thus bolstering the current arsenal for drug discovery. By harnessing the breadth of genomics at tree-of-life scale, the project aims to revitalize drug discovery techniques by introducing evolution-driven insights that might reshape the crafting of innovative and secure treatments. Moreover, its design holds the promise to develop into a PhD research agenda with potential to deliver tangible advancements in drug discovery when combined with artificial intelligence.

Professor Nicola Stanley-Wall

Professor Sarah Coulthurst

Biofilms have a significant impact in many environments including medical and agricultural sectors. Bacillus subtilis is a Gram-positive, spore-forming bacterium that is widely used as a model organism to increase our understanding of biofilm formation.

In this research project, the student will make use of the genetic diversity encoded within the B. subtilis pangenome to increase our knowledge of the mechanisms by which B. subtilis forms a biofilm and define how biofilm formation is impacted by environmental change, such as increased temperature. The student will use a collection of B. subtilis and closely related species, for which genome sequence data is available. The student will couple molecular biology with bioinformatics, imaging, and other physiological assays to further our understanding of this industrially and agriculturally important social behaviour.

Alongside developing your laboratory skills, you will be given training in data management and presentation skills and will be provided ample opportunities to develop other professional skills that you wish to enhance.

Dr Federico Pelisch

Accurate partition of the duplicated genome during cell division is crucial for cellular viability and organismal development. Chromosome mis-segregation is a major source of aneuploidy and it is a hallmark of cancer, while in oocytes represents the major source of miscarriages and genetic disease. As cells enter mitosis, chromosomes undergo compaction and establish specialized connections with spindle microtubules. The connection between chromosomes and microtubules is mediated by a proteinaceous structure that associates with chromosomal DNA, called the kinetochore.

Kinetochore composition and function needs to be tightly regulated during the cell cycle and kinetochore-specific kinases and phosphatases play a central role in this regulation. In spite of advances in the identification of such kinases and phosphatases as well as their targeting mechanisms, their specific substrates and roles during mitosis are poorly understood.

One key mitotic kinase involved in kinetochore function is polo-like kinase 1 (PLK1). While PLK1 plays critical roles during mitosis, how PLK1 achieves its different functions is not understood at the mechanistic level. Particularly, how PLK1 and counteracting phosphatases regulate kinetochore function through the different stages of mitosis is not clear. The aim of this research is to provide a mechanistic understanding of the chromosomal roles of PLK1 during mitosis by understanding how PLK1 phosphorylation of different kinetochore components impacts upon kinetochore function.

Davide Bulgarelli

Feeding a growing world population amid climatic modifications and international conflicts represents an unprecedent challenge for crop production. To achieve this task, we need to develop crops capable to adapt to the environment and in a timely fashion.

The microbial communities populating the interface between plant roots and soil, collectively referred to as the rhizosphere microbiota, can facilitate mineral nutrition and protect crops from pathogens, representing a renewable alternative to synthetic agrochemicals. These communities are not randomly assembled from soil: the host plant, akin to an orchestra conductor, contributes to define composition and function of the rhizosphere microbiota. Thus, resolving the molecular basis of plant-microbiota interactions may pave the way for a new generation of sustainable crops.

Speed breeding, a technique inspired by NASA’s approach at growing plants in space stations, recently gained centre-stage as an innovative strategy to accelerate crop development. Despite the research interest triggered by this approach, little is known on the impact of speed breeding on plant’s capacity of shaping the rhizosphere microbiota.

This Master by Research aims at filling this knowledge gap. Using barley (Hordeum vulgare), the world’s fourth most cultivated cereal and an excellent genetically tractable organism, as an experimental model, the student will compare the microbiota assembled by plants grown under speed breeding and “conventional” conditions. To achieve this task, the student will deploy cutting-edge experimental and computational approaches, strengthening new and existing skills in plant cultivation, microbial ecology, high throughput sequencing as well as statistical data analysis. Discoveries of the project will benefit the academic community, e.g., novel insights into host-microbe interactions, and stakeholders, e.g., breeding programme targeting the microbiota, alike.

Students with a passion for research who are motivated by a desire to contribute to sustainable crop production and decarbonisation of agriculture are the best fit for this project. The successful applicant will be based at the James Hutton Institute, a scientific campus on the outskirts of the city where the Dundee Plant Sciences and the newly established International Barley Hub (IBH) are located. The student will profit from the interactions with a diverse and multidisciplinary scientific community, including other post-graduate students, and state-of-the-art research facilities.

Further reading:

Escudero-Martinez and Bulgarelli (2023). Engineering the Crop Microbiota Through Host Genetics.

Hickey et al. (2019) Breeding crops to feed 10 billion.

Professor Kim Dale

During early embryogenesis, segments (somites) are formed during a process called somitogenesis. These somites will go on to form the bones and muscles of the skeleton. The timing of the segmentation process is regulated by a molecular oscillator, the segmentation clock, that drives cyclic gene expression with a periodicity that matches somite formation. This process is tightly controlled, and dysregulation of the segmentation clock results in diseases such as congenital scoliosis.

For the segmentation clock several levels of regulation of clock gene expression are important: transcriptional activation and negative feedback loops, post transcriptional regulation (from splicing to RNA stability) and protein degradation. Very little is known about the post transcriptional regulation in the segmentation clock, however it is of critical importance for the function of another molecular oscillator, the circadian clock where post transcriptional regulators include RNA binding proteins (RNA-BPs) and microRNAs (miRNAs).

This project will investigate how these post transcriptional regulators control the segmentation clock and the formation of somites in human induced pluripotent stem cell (hiPSC) derived presomitic mesoderm (PSM) cells as well as in hiPSC derived 3D structures called somitoids. It will provide insights into the mechanisms required for accurate segmentation clock gene expression in embryonic development as well as diseases associated with misregulation of the segmentation clock or the signalling pathways involved such as congenital scoliosis and T-cell acute lymphoblastic leukaemia (T-ALL).

Aims of the project:

Identify the RNA-BPs and/or miRNAs that interact with clock gene mRNAs
Determine the post transcriptional mechanisms that regulate clock gene mRNAs
Establish how this impacts somitogenesis

Examples of techniques expected to be used during the project: maintenance of hiPSC, CRISPR modification of hiPSC, differentiation of hiPSC into PSM cells, generation of hiPSC derived somitoids, immuno fluorescence, in situ hybridisation, microscopy (e.g. time lapse imaging, confocal), purification of DNA, RNA and protein, RT-qPCR, Next Generation Sequencing (e.g. RNAseq, RIPseq, miRNASeq, RIBOseq, TAILseq, scSeq), immuno precipitation, western blotting, mass spectrometry, analysis of large data sets.

Professor Alessio Ciulli

Recent advances from the Ciulli Lab and others have contributed to the establishment of a transformative new modality of chemical intervention into biological system – one that moves beyond the state-of-the-art. Instead of blocking a target protein with conventional inhibitors, we are now designing and studying “tailored” molecules, multi-specific in concept and function, that bring two or more proteins together by forming a ternary (or higher order) complex. We have shown that specific molecular recognition features of such ternary complexes, such as their cooperativity and thermodynamic and kinetic stability, are a key feature of their “molecular glue” activity, and drive fast and effective induce proximity-driven chemistries. For degrader molecules that co-opt E3 ligases to target protein, this specifically relates to protein ubiquitylation and subsequent proteasomal degradation. We are beginning to understand the rules of how to design and study this new class of molecules in order to best re-wire specific downstream signalling events, with profound biological consequences and attractive therapeutic potential.

Our research in this area takes a multidisciplinary approach including organic and medicinal chemistry and computational tools to design and achieve desired molecules; biophysics and structural biology, including the use of cryo-electron microscopy, to study binary and ternary complexes in solution and reveal their structural and dynamic interactions; and chemical biology, biochemistry, proteomics and cell biology to study the cellular impact of our small molecules in relevant cellular systems – for example cancer cells sensitive to the knockdown or other modification of the protein target in question.

The key long-term research questions of the project will be: how to best identify protein pairs that have intrinsically basal affinity and surface complementarity, and understand how to use that information to accelerate the discovery and more rational design of molecular glues. A one-year Master project would typically fit as part of an on-going project and research interest of the Lab. Importantly; it can be tailored to the student specific interests and motivations.

The student will join a vibrant research group led by Professor Ciulli who is the Director of the Centre for Targeted Protein Degradation and has extensive experience of supervising students. He/she will benefit from access to excellent expertise, facilities, and support that will prove invaluable for their scientific and professional development. The group and wider CeTPD have lot of collaborations with industry which will also advance the student’s personal and professional development beyond what is possible through an academic-only Master project.

If you are interested in joining the lab and contributing to our science in this exciting new area, to learn more about our work and to discuss potential opportunities, do not hesitate to get in touch with Alessio ([email protected]).

Recent references

Liu, X., Ciulli, A.*

Proximity-Based Modalities for Biology and Medicine

ACS Cent. Sci. 2023, 9 (7), 1269–1284

Hsia, O. et al.

Targeted protein degradation via intramolecular bivalent glues.

Nature2024, 627 (8002), 204–211.

Kroupova, A. et al.

Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders.

Nat Commun.2024 Oct 15;15(1):8885.

Dr Greg Findlay

The overarching goal of this project is to identify and characterise protein kinase signalling pathways that are disrupted in human neurodevelopmental disorders. This research will uncover new therapeutic targets and avenues that might be used in treatment of patients these debilitating disorders.

Protein kinases function as reversible switches in signal transduction and as such are fundamental regulators of all cellular processes. A major role for protein kinases during human development is controlling differentiation of adult tissues and organ, such as the brain. As a result, protein kinase signalling pathways are frequently dysregulated in human neurodevelopmental disorders. Because protein kinase activity can be specifically and reversibly manipulated using chemical tools for therapeutics and tissue engineering, there is a pressing need to identify relevant protein kinase circuits. However, beyond several notable examples, protein kinase pathways, regulatory mechanisms and molecular functions that control human neurodevelopmental processes remain poorly understood.

Ser-Arg Protein Kinase (SRPK) has been known for many years to phosphorylate splicing factors to promote spliceosome assembly and mRNA splicing. However, we recently showed SRPK has acquired splicing independent functions during human development. SRPK phosphorylates the E3 ubiquitin ligase RNF12/RLIM to pattern gene expression programmes required for neurodevelopment, whilst genes encoding SRPK-RNF12 pathway components are mutated in a series of related human neurodevelopmental disorders including Tonne-Kalscheuer syndrome (TOKAS). These data suggest that the SRPK pathway plays a key role in neurodevelopmental regulation, and that dysregulated SRPK signalling may underpin human neurodevelopmental disorders.

The goal of this project is to identify novel SRPK substrates that are relevant for human neurodevelopment by state-of-the-art global phosphoprotemic profiling of human induced pluripotent stem cell (hiPSC)-derived neural cell types. The student will explore mechanisms by which SRPK phosphorylation regulates molecular functions of key substrates, and how newly identified SRPK signalling pathways control downstream neurodevelopmental processes using hiPSC models. Finally, they will determine whether and how the SRPK signalling pathways are disrupted in patients with neurodevelopmental disorders.

This project offers a unique opportunity to illuminate new molecular mechanisms underpinning human neurodevelopment that are disrupted in disease.

Selected recent Findlay lab publications:

Espejo-Serrano et al (2024) Chromatin targeting of the RNF12/RLIM E3 ubiquitin ligase controls transcriptional responses. Life Sci Alliance. 10;7(3):e202302282. doi: 10.26508/lsa.202302282.
Hogg EKJ & Findlay GM. (2023) Functions of SRPK, CLK and DYRK kinases in stem cells, development, and human developmental disorders. FEBS Lett. 597(19):2375-2415. doi: 10.1002/1873-3468.14723.
Bustos F & Findlay GM (2023) Therapeutic validation and targeting of signalling networks that are dysregulated in intellectual disability. FEBS J. doi: 10.1111/febs.16411
Segarra-Fas A et al (2022) An RNF12-USP26 amplification loop drives germ cell specification and is disrupted by disease-associated mutations. Sci Signal. 15(742) doi: 10.1126/scisignal.abm5995
Bustos F et al (2022) Activity-based probe profiling of RNF12 E3 ubiquitin ligase functions in Tonne-Kalscheuer syndrome. Life Sci Alliance. 5(11) doi: 10.26508/lsa.202101248
Bustos F et al (2021) A novel RLIM/RNF12 variant disrupts protein stability and function to cause severe Tonne-Kalscheuer syndrome. Sci Rep. 11(1):9560 doi: 10.1038/s41598-021-88911-3.
Bustos F et al (2020) Functional diversification of SRSF protein kinase (SRSF) to control ubiquitin-dependent neurodevelopmental signalling. Dev Cell. 55(5), 629-647 doi: 10.1016/j.devcel.2020.09.025.
Fernandez-Alonso R et al (2020) Phosphoproteomics Identifies a Bimodal EPHA2 Receptor Switch that Promotes Embryonic Stem Cell Differentiation. Nat Commun. 11(1): 1357. doi: 10.1038/s41467-020-15173-4
9. Bustos F et al (2018) RNF12 X-linked intellectual disability mutations disrupt E3 ligase

activity and neural differentiation. Cell Rep. 23(6): 1599-1611

Dr Adrien Rousseau

The Rousseau lab is interested in decoding how protein degradation by the proteasome is regulated in cells so that accumulation of unfolded, misfolded, or damaged proteins can be cleared before they become deleterious. The proteasome recognises, unfolds, and degrades faulty proteins that have been tagged with ubiquitin to maintain the integrity of the proteome. Defects in the proteasome give rise to various human diseases, such as cancer and neurodegenerative disorders. We recently reported that proteasome assembly and activity is increased upon various stresses to help rewire the proteome and survive. We now study the spatio-temporal regulation of proteasome assembly and activity in health, stress and diseases using both yeast and mammalian systems. This includes assembly of the poorly characterised alternative forms of the proteasome.

The MSc project aims at engineering the proteasome to develop new technologies to rapidly monitor assembly of its alternative forms. This will be instrumental in better understanding the function of alternative forms of the proteasomes and may help understand their involvement in diseases. The project will offer training opportunities in state-of-the-art technologies such as high-resolution confocal microscopy (proteasome dynamics), molecular biology (proteasome and protein degradation assays), and cell engineering (CRISPR-Cas9 gene editing of proteasome genes).

Dr Dan Neill

Bacterial pathogens respond rapidly to environmental change, in ways that can influence their growth, virulence, antimicrobial resistance and, therefore, infection outcomes. The ability to adapt to changing conditions is intrinsically linked to environmental sensing systems that respond to local physical, chemical and biological cues. A key trigger for many bacterial pathogens is temperature change. Sudden increases in local temperature are associated with initial colonisation of a host and with movement from peripheral to internal host niches. Exploring how bacterial pathogens sense and respond to temperature change can help us understand disease mechanisms and may pave the way to future therapeutic interventions.  

Using the major human respiratory pathogen Streptococcus pneumoniae as an exemplar, this project will explore how temperature influences pathogen gene expression at the transcriptional and post-transcriptional level, and how this leads to phenotypic change that affects antimicrobial resistance, virulence and pathogenesis. Using transcriptomic, molecular genetics and infection biology approaches, the student will identify genes that are differentially regulated by temperature and will explore how their protein products contribute to adaptation to host conditions. Temperatures associated variously with the external environment, the upper airways, core body temperature and fever will be considered. The student will have the opportunity to analyse large transcriptomic datasets, to generate and characterise bacterial mutants and to explore host-pathogen interactions in in vitro infection studies with mammalian cells.

Disease caused by Streptococcus pneumoniae disproportionately affects the global south, including regions in which heat waves are a regular phenomenon, and one associated with increased demands on public health services. Improved understanding of the relationship between temperature and bacterial disease has potential to inform mitigation strategies and to pave the way for novel treatments. 

Dr Sarah McKim

Plants living on land face brutal threats from pests, dehydration and temperature. To survive and thrive, land plants evolved a waxy ‘cuticle’ and distinctive epidermal cells such as gas pores and defensive barbs. Further changes to the epidermis help cereal performance on arid grasslands and play important roles in climate resiliency. However, we understand little about how plants, including cereals, coordinate multiple innovations on the epidermis into a coherent surface.

Excitingly, we recently discovered a core patterning pathway controlling epidermal development in cereals (1). In this project, the student will advance these findings using state of the art biochemical and molecular approaches to find out how the pathway components interact and respond to environmental change. This project will appeal to students keen to explore plant science from molecule to field, and to contribute to crop improvement and food security. In this project, the student will learn the latest molecular biology, cereal physiology and development and protein biochemistry methods.

The student will be based in the McKim lab, a dynamic, productive and supportive research group studying cereal development, which is based at the James Hutton Institute (JHI), a global leader in cereal genetics and genomics, and part of the International Barley Hub, a £62 million investment in cereal research. The student will participate in training offered both by University of Dundee and JHI, and join a cohort of next-generation cereal scientists. We warmly welcome students from diverse backgrounds and cultures. Please feel free to contact me to discuss any aspects of the project.

Liu et al (2022) Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley. Nat Commun. 2022 Oct 13;13(1):6050. doi: 10.1038/s41467-022-33300-1 https://rdcu.be/cZJHd

Dr Varsha Singh

Parkinson’s Disease or PD is the second fastest growing neurodegenerative disease in the UK. PD is an age-associated disease characterized by tremors, change in gait, loss of appetite and loss or reduction in the sense of smell (anosmia). Anosmia is reported in individuals with PD years to decade before tremors and loss of dopaminergic neurons. Anosmia has a huge impact on the quality of life leading as well as loss or gain in body weight. Mutations in a gene encoding a leucine rich repeat kinase, LRRK2, are linked to (i) familial cases of PD, (ii) loss of cilia in neurons. Individuals with PD carrying pathogenic mutations in this gene also report anosmia.

To obtain mechanistic insight into anosmia, we will create a genetic model for PD in a nematode Caenorhabditis elegans where we have well established assays to study olfaction and cilia morphology. In the M Res research project, we will express mutant copy of human lrrk2 gene in ciliated, olfactory neurons of C. elegans and study their effect on cilia morphology, odorant structure expression and receptor function in whole animals. In humans and mice, LRRK2 is known to phosphorylate Rab GTPases involved in vesicular trafficking. We will study phosphorylation patterns for C. elegans Rab proteins in presence of pathogenic LRRK-2 protein.

The student will acquire training in C. elegans maintenance, genetic manipulation, microscopy-based imaging of olfactory neurons, chemotaxis assays, transcript analysis by qRT-PCR and analysis of proteins by gel electrophoresis and Western Blotting. The student will be provided training in scientific writing, statistics and data management. The student will also receive mentoring support during career transition.

Dr Virginia De Cesare

Ubiquitylation, the process by which the small protein ubiquitin is attached to target proteins, is a fundamental post-translational modification (PTM) that regulates almost every cellular function. Dysregulation of the ubiquitylation machinery is implicated in numerous diseases, including cancer, neurodegenerative diseases, and immune dysfunctions. Traditionally, ubiquitylation was believed to occur exclusively on lysine residues (canonical ubiquitylation). However, recent ground breaking discoveries have revealed that ubiquitin can also be attached to other amino acids, such as serine and threonine, as well as non-protein molecules like sugars (non-canonical ubiquitylation).

Non-canonical ubiquitylation challenges established paradigms in protein regulation and opens new avenues for understanding cellular functions in health and disease. Understanding the scope and biological significance of non-canonical ubiquitylation will reshape our knowledge of cellular processes and identify novel therapeutic targets.

This MSc by Research project will address key questions, including:

What is the extent and distribution of non-canonical ubiquitylation in cells?
What are the biological roles and regulatory mechanisms of non-canonical ubiquitylation?
How does non-canonical ubiquitylation influence disease processes, particularly in cancer?

We offer several well-defined, self-contained projects tailored to the specific interests and career goals of the student, each emphasizing the development of specialized skill sets:

Mass Spectrometry & Proteomics: Identify novel targets of non-canonical ubiquitylation, leveraging state-of-the-art proteomics tools to uncover new mechanisms of protein regulation.
Protein Biochemistry & Structural Biology: Reconstitute and analyse the non-canonical ubiquitylation machinery, defining its structure and elucidating its function using biochemical and structural methods.
Molecular Biology & Gene Editing: Investigate the role of non-canonical ubiquitylation in cancer cell lines, exploring its impact on cellular pathways and disease progression.
If you’re highly motivated and excited to be part of this innovative research, contact Virginia ([email protected]) to learn more or to apply.

Dr Tony Ly

Age-associated physiological decline is characterized by loss of resilience towards stress and injury. Understanding mechanisms of resilience is a global challenge due to the demographic shift towards aging populations. Cellular senescence is a clinically important phenotype that is both pro-aging and tumor suppressive. Senescence is fundamentally characterized by durable cell cycle arrest in response to replicative aging and cellular stresses. This phenotype was originally described in primary fibroblast cells, which cease proliferation after prolonged culture in vitro. However, it is now recognized that many cell types senesce in response to various cellular insults, including DNA damage and oncogene activation. Understanding mechanisms that promote cellular senescence will be key to identifying approaches to prevent, reverse or eliminate senescent phenotypes.

The Ly laboratory identified a novel ‘cell overgrowth’ mechanism that promotes senescent phenotypes. In response to cell cycle arrest, continued cell size increases results in cell overgrowth and imbalanced scaling of the cell proteome resulting in a cellular stress response and ultimately senescence.

This imbalanced proteome scaling is characterized by altered ratios of cell organelles and major changes in the bulk physicochemical properties of the proteome. Senescent phenotypes can be reversed by inhibiting cell growth, indicating that the cell overgrowth is the cause.

While senescent cells are nearly universally dysmorphic, their cell size can either be smaller or larger than the parental non-senescent cell. Indeed, we have discovered genetic perturbations resulting in senescent cells with decreased cell size. We hypothesize that imbalanced proteome scaling occurs in both aberrantly small and large senescent cells, and it is the aberrant scaling, not size per se, that promotes senescence. If true, this would be a unifying mechanism of cellular senescence. To test this hypothesis, the Masters project will unpick the mechanisms linking aberrant size and cellular senescence using genetically tractable in vitro models, advanced proteomic technologies and data analysis pipelines for the interpretation of large datasets.

Specific aims:

Generate novel in vitro epithelial models of cellular senescence using genome editing
Apply cutting edge proteomics technologies enabled by state-of-the-art mass spectrometry instrumentation to characterize proteome scaling in senescent cells
Use CRISPR/Cas9 and inducible protein degradation to interrogate mechanisms of cellular senescence

The expected impacts of this research will support the identification of pathways that can be further explored as targets to prevent or reverse senescent phenotypes. The results will potentially reveal a unifying mechanism linking aberrant cell size regulation and senescence.

Dr Varsha Singh

Gut microbiome is the community of microbes living together in the gastrointestinal tract of an animal. They provide specific functions to the animal host such as digestion of cellulose and protection from invading pathogens. Large scale sequencing analyses have led to identification of several bacteria, some archaea and fungi in various animals including humans. It is not clear if various microbes in the microbiota of a specific animal are similar or the combined metabolic output of microbiota in various animals is similar. This can be examined by studying secondary metabolites produced by the microbiotas of different animals. In this MRes research project, we will identify volatiles chemicals (odours) produced by microbiota of a nematode (Caenorhabditis elegans), a fruit fly (Drosophila melanogaster) and mice by Gas Chromatography mass spectrometry (GC-MS/MS). This will allow us to determine if their microbiota produces unique or overlapping odours. Further, we will identify microorganisms in the gut of C. elegans and Drosophila melanogaster, and in faeces of mice by metagenomics.

The student will acquire training in microbiology, C. elegans and fruit fly maintenance, GC-MS analysis of individual bacteria and complex samples such as mouse faeces. The student will be provided additional training in scientific writing, statistics and data management. The student will also receive mentoring support during career transition.

Dr Claudia Martinho

In plants, phenotypic innovation is not exclusively encoded in DNA sequences. Some heritable new traits are associated with modifications on the DNA, such as DNA methylation. DNA methylation involves the binding of methyl groups to cytosines in the DNA molecule. High DNA methylation levels cause transcriptional gene silencing (TGS) and switch genes off. Because this type of regulation is independent of DNA sequences it is referred to as epigenetic.

In most cases DNA methylation is inherited in a Mendelian fashion. However, DNA methylation can be transferred between homologous alleles. This type of communication between alleles is referred as paramutation and it violates Mendel’s first law of segregation.

Recently, it was found that a DNA methyltransferase (CMT3) and Histone methyltransferase (KYP) are required to maintain paramutation in a model for paramutation in tomato (sulfurea) across generations1. However, the mechanisms underlying the establishment of paramutation remain poorly understood.

How can an epigenetic mark be transferred from one locus to the other in somatic cells after fertilization? To address this question, we hypothesize that proteins involved in the establishment of epigenetic marks might be involved in this process. These include proteins involved in generating small RNAs since in plants these RNA molecules initiate DNA methylation. In this project the student will design, carry out in vitro validation and generate constructs to knock-out proteins involved in sRNA generating pathways in tomato.

In addition, we recently found that cis regulatory regions might be required to establish paramutation (unpublished). How are these cis regulatory regions regulated and how do they affect paramutation? We hypothesize the DNA methylation status of cis regulatory regions affects paramutation at the sulfurea locus. To test the effect of these epigenetic marks the student will transiently transfect plant cells with DNA demethylases2 targeted at sulfurea and analyze its status. Once this transient system is established other hypotheses can be tested.

This project will employ genetics, biotechnology and molecular biology to shed light on one of the oldest and unsolved mysteries in plant genetics but also provide valuable technical expertise in crop science and biotechnology.

References

1. Martinho, C. et al. CHROMOMETHYLTRANSFERASE3/KRYPTONITE maintains the sulfurea paramutation in Solanum lycopersicum. Proceedings of the National Academy of Sciences 119, e2112240119 (2022).

2. Gallego-Bartolomé, J. et al. Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain. Proceedings of the National Academy of Sciences 115, E2125–E2134 (2018).

Dr Peter Cossar

Molecular glues, small molecules that facilitate the assembly of biomolecular complexes, have emerged as a transformative drug discovery strategy for treating diseases such as cancer and neurodegeneration. Their gain-of-function mechanism has demonstrated remarkable therapeutic potential. Among these, molecular glue degraders are the most well-characterized approach, highlighting the significant promise of this drug technology.

However, this represents only the tip of the iceberg for this drug discovery technology.

Cancer cells often employ strategies to destabilize critical regulatory proteins, such as the tumour suppressor p53. This destabilization frequently arises from point mutations that lead to protein degradation, allowing cancer cells to bypass essential regulatory checkpoints. Stabilizing these mutated proteins by capturing them within biomolecular complexes offers a compelling opportunity to restore tumour-suppressor function.

In this master’s research project, you will explore a molecular glue stabilizer approach to enhance p53, and it’s isoforms, with its interact endogenous partner proteins.

In this research project you will.

Screen and identify the hit molecules that bind to the tumour suppressor complex.
Biophysically and structurally characterize tumour suppressor complex stability.
Develop a structural-activity relationship to investigate cooperative multi-component complex assembly
Study how molecular glue stabilization influence protein stability in vitro.

The Cossar Lab, based within the Centre for Targeted Protein Degradation at the University of Dundee, provides a multidisciplinary environment with world-class facilities. Here you will be exposed to both academic and industry scientist across the breadth of Medicinal Chemistry to Cellular Biology. This includes exposure to researchers from leading biotechnology companies such as Boehringer-Ingelheim, Eisai, and Tocris.

This project will equip you with expertise in organic synthesis, biophysical assay screening, protein production, and small-molecule design. Through a combination of hands-on research and collaborative opportunities, you will develop an in-depth understanding of molecular biophysics, chemical biology, and drug discovery. Training will also focus on professional development, including presenting your scientific work, collaborating within multidisciplinary teams, networking, and scientific writing.

The Cossar lab research uses molecular glue-, covalent-, and fragment-based drug discovery approaches to address intricate biological questions, giving you a comprehensive training experience.

The successful candidate will have foundational knowledge in drug discovery, synthetic chemistry, or chemical biology. While the project focus areas can be tailored to your interests, you will receive dedicated support in honing technical skills and professional competencies.

The University of Dundee’s inclusive research community is an ideal setting for ambitious individuals. We welcome applications from all talented candidates, particularly those with the drive and potential to make a significant impact in the field of drug discovery.

Professor Philip Cohen

The accumulation and precipitation of unbranched glycogen in human tissues as toxic polyglucosan bodies (PB) underlies four human diseases that cause cardiomyopathy and heart failure and/or fatal neurological disorders. They result from mutations in the genes encoding the E3 ubiquitin ligases HOIL-1 or Malin, or the Malin-interacting protein Laforin, or from deficiency of glycogen branching enzyme (GBE1) or the glycogen synthesis priming protein glycogenin-1 (GYG1).

We discovered that HOIL-1 is an unusual E3 ligase that attaches ubiquitin to the hydroxyl side chains of serine and threonine residues in proteins https://www.pnas.org/doi/epdf/10.1073/pnas.1905873116 and to the C6 hydroxyl groups of glucose residues in unbranched glycogen https://doi.org/10.15252/embj.2021109700 . These and other observations led us to propose that the HOIL-1-catalysed monoubiquitylation of unbranched glycogen leads to its polyubiquitylation by the malin-laforin complex and perhaps other E3 ligases, resulting in the elimination of the unwanted, toxic, unbranched glycogen by an autophagic mechanism.

Recently, we made demonstrated for the first time unbranched glycogen formed in GBE1 knockout (KO) human cells is polyubiquitylated, but normally branched glycogen formed in the parental wild type cells is not. The aim of the project is to investigate whether the abnormal glycogen formed in GYG1 KO cells is ubiquitylated and transported to lysosomes for destruction by lysosomal acid alpha 1:4 glucosidase by the same mechanism as the unbranched glycogen formed in GBE1 KO cells.

The project will involve making GYG1 KO cells, HOIL-1/GYG1, Malin/GYG1 and Laforin/GYG1 double KO cells by CRISPR/Cas9 gene editing technology followed by isolation of the glycogen formed in these cells. The polyubiquitin chains attached to glycogen in GYG1 KO cells will be analysed to identify the different ubiquitin linkage types present, and compared to the ubiquitylated, unbranched glycogen formed in GBE1 KO cells. If time permits, the mechanism by which polyubiquitylated unbranched glycogen is transported to lysosomes will also be elucidated. These studies will help to establish whether every disease caused the accumulation and precipitation of PB (i.e. in patients deficient in HOIL-1, malin, laforin, GYG1 or GBE1) can be explained by a common underlying mechanism.

The research challenges current dogma that ubiquitylation is confined to proteins, and promises to establish sugar ubiquitylation as new quality control mechanism for the elimination and hydrolysis of unwanted, toxic unbranched polysaccharides from cells.

Dr Martin Balcerowicz

In our warming climate, understanding how plants respond to elevated temperatures is vital for breeding temperature-resilient crops. While many genes involved in the temperature response have been discovered in the model plant Arabidopsis thaliana, it remains unknown whether they contributed to adaptation to various climates across natural Arabidopsis accessions.

In the Balcerowicz Lab, we are currently investigating novel regulators of the plant temperature response that are controlled by upstream open reading frames (uORFs). uORFs are short sequences located upstream of a transcript’s main coding region and are generally considered negative regulators of mRNA translation. Few uORFs have been linked to biotic and abiotic stress responses, and so far, none are known to regulate responses to above-optimal ambient temperature. Natural variation in some of these uORFs exist amongst a range of Arabidopsis accessions (https://1001genomes.org/).

This project aims to determine the impact of uORF natural variation on the plant’s temperature response using genetic and molecular biology techniques. The student will characterise the function of uORF variants in the process of translation using site-directed mutagenesis and in vitro translation assays, and they will study the temperature response across a range of natural accessions, investigating variation in phenotype as well as in gene expression (using qPCR) and protein accumulation (using Western blotting).

Dr Didier Ndeh

Plant cell wall glycans are a major component of plant biomass, essential for plant physiology, development, and protection against environmental stress and disease. They also provide raw materials for valuable economic products, including wood, textiles, paper, biofuels, and food additives such as gelling and thickening agents. Additionally, they serve as dietary fiber, which supports human nutrition and immune health. Due to their abundance and potential, plant glycans have become a focus of extensive research to better understand their structure and metabolism (both biosynthesis and degradation) and to develop methods to manipulate them. Such research could inform biotechnological applications, helping to improve plant health as well as reduce our dependence on plastics, fossil fuels and promoting healthier, more sustainable living. Progress in this field is however hindered by several challenges, including the complexity of glycan structures and purification approaches, high costs, low extraction yields, and limited biochemical and genetic tools.

In this project, we aim to develop, test, and optimize methods for extracting and purifying plant cell wall glycans using a combination of microbial enzymes, genetically engineered microbes, glycan-degrading enzymes, and other chemical reagents.

We will also characterize their structure and investigate the metabolism in the contexts of plant health and disease.

The student will gain hands-on experience with a range of techniques, including gene cloning, protein expression and purification, microbial culturing and genetic modification and glycan analysis using mass spectrometry, nuclear magnetic resonance (NMR) spectroscopy, and structural biology.

Dr Henry McSorley

Parasitic helminths (worms) are master manipulators of the immune system: they secrete multiple proteins which interact with cells and cytokines of the immune response, inhibiting or skewing the response towards an outcome more favourable to them. Recent work from our lab and others has identified multiple secreted proteins which act to alter the immune system. These proteins include HpARI, which binds and modulates the cytokine IL-33, HpBARI, which binds and blocks the IL-33 receptor ST2, and Hp-TGM, which binds and activates the host TGF-beta receptor. HpARI, HpBARI and HpTGM are all members of multi-gene families, each of which have different effects on their targets. These activities are insufficiently characterized, and the role of these proteins in infection are still unclear.

There are also multiple further immunomodulatory activities identifiable in parasite secretions which have not been paired to an individual defined protein. We aim to identify further immunomodulatory proteins from helminth parasites, which have the potential to modulate immune responses in immune-mediated disease, and could act as vaccine antigens against parasite infections.

In this project, we will use proteomic analysis of parasite secretions, recombinant mammalian cell expression of candidate proteins, in vitro immunological assays and protein-protein interaction assays to further characterize the activities of known and novel parasite immunomodulatory proteins.

Dr Rastko Sknepnek

It is an important question to answer how cells move in a crowded environment.

In this project, we’ll use the vertex model (a widely used computational framework for cell-based studies of epithelial tissue mechanics) to study motion of a small patch of motile cells in otherwise inert environment.

The student will learn how to set up and run a sophisticated numerical simulations of a model biological system.

She/he will also gain skills on how to work with complex research computer codes, analyse simulation data and produce publication-quality plots.

In addition, the student will gain considerable working experience with programming in Python and with using UNIX-based high-performance computing facilities.

Basic knowledge of physics, mathematics (including calculus), and Python programming is required.

Dr Constance Alabert

DNA replication is required for successful cell fate transitions across diverse physiological, experimental, and pathological contexts, involving factors often deregulated in human cancer and intellectual disabilities. The underlying mechanisms are fundamental for our understanding of organ homeostasis but are poorly understood. We have discovered a profound and rapid rewiring of the proteins that are recruited around DNA replication forks, upon differentiation of human induced pluripotent stem cells (iPSCs) into mesoderm. A large proportion of these proteins are epigenetic regulators that are potential driver of differentiation. The aim of this project is to explore the specific role of these epigenetic regulators in cell fate decisions.

To do so, we will develop a new technology to achieve targeted protein degradation specifically at replication forks. Using this approach, we will monitor changes in chromatin accessibility (ATAC-seq), and histone modifications (iPOND-MS). In parallel, using an established protocol in the lab, changes in nuclear organization and cell cycle remodelling will be assessed by quantitative high-throughput single cell imaging. In conclusion, this project encompasses a blend of discovery approaches using mass spectrometry and mechanistic studies to reveal how DNA replication contributes to the mechanistic diversity of cell fate transitions.

Professor Karim Labib

The process of chromosome replication is defective in many cancer cells, which therefore have an increased dependency on pathways that allow cells to survive ‘DNA replication stress’. Drugs inhibiting such pathways have great potential in the clinic - the best example is the ATR kinase that activates the ‘DNA damage checkpoint pathway’, which is essential for the survival of cells experiencing DNA replication stress. ATR inhibitors are currently in Phase II trials as anti-cancer agents, but cancer cells can develop resistance to such inhibitors, making it important to identify additional pathways to inhibit, with a different mechanistic basis to ATR and the DNA damage checkpoint.

Genome-wide CRISPR knockout screens indicate that mutation of the USP37 deubiquitylase makes cells just as sensitive to DNA replication stress as inhibition of ATR. At present, it is unclear how USP37 protects cells from DNA replication stress, or what are the relevant targets of USP37 when chromosome replication is defective. In our ongoing work, we have found that USP37 counteracts the action of two ubiquitin ligases that act at DNA replication forks. These are CUL2LRR1 and TRAIP, which jointly control the ubiquitylation and disassembly of the chromosome replication machinery in mammalian cells. Until now, however, it is unclear which targets of CUL2LRR1 or TRAIP might be protected from ubiquitylation by USP37 during DNA replication stress.

After purifying USP37 from mammalian cells, we found by mass spectrometry that it interacts with two large protein complexes. One is the replisome (the chromosome replication machinery) and the other is the cohesin complex that holds sister chromatids together before mitosis. This suggests that USP37 might protect cells from DNA replication stress by preventing premature ubiquitylation of the replisome, or by counteracting cohesin ubiquitylation to preserve genome integrity. The role of cohesin ubiquitylation has not previously been determined and so is a very interesting question for exploration.

In this project, we will explore the molecular basis and functional implications of cohesin ubiquitylation in mammalian cells. Using a combination of cutting-edge genetics, biochemistry and cell biology, we will try to identify which enzymes carry out cohesin ubiquitylation (e.g. CUL2LRR1, TRAIP, or other ubiquitin ligases), determine how USP37 counteracts cohesin ubiquitylation, and explore the functional implications. This will involve a multi-disciplinary approach using techniques as CRISPR-mediated genome editing, protein purification, DNA cloning & sequencing, mass spectrometry, advanced imaging, structural predictions via AlphaFold, and biochemical validation of predicted interactions. Cells lacking USP37 are highly sensitive to ATR inhibitors, and a deeper functional characterisation of USP37 will help to reveal its potential as a target for new anti-cancer therapies.

Professor Ulrich Zacharaie

Ion channels are key components in every cell, bridging cell and organellar membranes for the traversal of charged species. Calcium channels are of particular physiological importance because of the central role calcium plays in cell signalling and cell death. They are also essential for the replication and maturation of viruses in host cells. For these reasons, many drugs and drug candidates target calcium channels.  

A better understanding of the function of calcium channels is needed to underpin the design of safe, efficient drugs. In this project, you will investigate the mechanisms of biomedically important calcium channels by a combination of molecular modelling, biomolecular simulations, and ligand docking. A special focus will be placed on therapeutics that may inhibit the flow of ions through the channel. You will acquire training in computational biology and computational chemistry techniques as well as data analysis and predicting molecular properties including by machine learning. The results of your work will inform drug design programmes in both academia and industry.  

References: 

Ives et al., J Gen Physiol (2023) 155: e202213226. 
Şahin and Zachariae, biorxiv (2023) 2023.11.01.565142.

Catterall et al., Ann Rev Pharmacol Toxicol (2020)60:133-154. 

Dr Hajk-George Drost

In this computational Master project, we will consult new transcriptomic evidence from bulk- and single cells (single-cell genomics) to test whether evolutionary information of gene birth events within the tree of life can be harnessed to inform transcriptomic signatures for cancer type diagnostics (evolutionary transcriptomics).

The expected impact of this project is to derive a quantitative evolutionary transcriptomic metric to classify temporal transcriptome datasets from various types and stages of cancer through their distinct patterns of gene age and transcript abundance. To achieve this, the ideal candidate will learn cutting-edge AI and software solutions developed in our team (myTAI, Drost et al., 2018; DIAMOND2, Buchfink et al., 2021; DeepClust, Buchfink et al., 2023; and GenEra, Barrera-Redondo et al., 2023) to establish a new evolutionary transcriptomics framework for cancer diagnostics. The successful candidate will make active contributions to the emerging field of evolutionary medicine which is concerned with introducing evolutionary information to established molecular diagnostics methodologies.

The main question that this research project will address is whether evolutionary transcriptomics can be used ass classification method to distinguish different states of cell differentiation (Quint, Drost et al., 2012; Drost et al., 2015; Drost et al., 2016; Drost et al., 2017; Lotharugkpong et al. 2024 and cancer formation (Trigos et al., 2017). 

This project will also introduce the candidate to our collaborators at the University of Cambridge and at the Max Planck Institute for Biology in Tuebingen, Germany.

Professor Gopal Sapkota

Cancer and neurodegenerative diseases are among the most challenging conditions to treat, and as life expectancy increases globally, the burden of these diseases continues to rise. Traditional therapies often focus on developing small molecule inhibitors or activators that target disease-causing proteins. However, many of these proteins do not function as enzymes with well-defined activities, making them difficult to target directly. These are often referred to as "undruggable" targets.

The Sapkota Lab has pioneered a range of proximity-inducing platforms to overcome this challenge, including the Affinity-directed PROtein Missile (AdPROM) system (PMIDs: 28490657, 32668202) and the BDPIC (bromoTAG-dTAG proximity-inducing chimera) system (PMIDs: 39104417; 39081292). These systems leverage targeted recruitment of enzymes to modify the post-translational status of intracellular proteins, thereby altering their functions. For example, by recruiting an E3 ligase to the oncogenic protein K-RAS, we can induce its degradation via the ubiquitin-proteasome pathway (PMIDs: 37591251, 32668202, 32668203). Similarly, by recruiting protein phosphatases to phosphorylated proteins, we can dephosphorylate these proteins, modulating their activities and potentially altering disease progression (PMIDs: 39104417; 39081292, 36720221).

The MRes research projects in the Sapkota Lab aim to provide proof-of-concept for novel approaches to modify the function of proteins implicated in cancer and neurodegenerative diseases through targeted post-translational modifications. Students will be trained in cutting-edge techniques in cell and molecular biology (including CRISPR/Cas9 genome editing), biochemistry, proteomics, and synthetic chemistry to engineer effective strategies for targeted modification of intracellular proteins. This could lead to the development of innovative therapeutic strategies to potentially tackle these devastating diseases. Furthermore, as the Sapkota Lab collaborates with leading pharmaceutical companies, promising findings will be translated into collaborative drug discovery projects with industry partners, potentially accelerating the path from bench to bedside.

Dr Jorunn Bos

Pests and diseases are a major threat to food security with losses ranging between 20-40%. Aphids are one of the most devastating insect pests, globally. These insects form a close association with their host and use specialized mouthparts (stylets), to probe leaf tissue and feed on the phloem over prolonged periods of time. Upon puncturing the leaf epidermis, the stylets follow a mainly extracellular route through the different cell layers to reach the phloem, and puncture cells along the pathway. During probing and feeding, saliva is secreted, which is rich in proteins and small molecules that function as effectors in reprogramming host processes underlying susceptibility

Functional characterization studies have implicated several effectors in aphid virulence, indicating that they are important players in plant-aphid interactions. In our bid to attribute function to an increasing number of candidate effectors, the identification of their cellular host targets represents a critical step. We previously initiated an aphid effector host target identification approach to determine the role of effectors in manipulating host cell processes. This project will focus validation and characterization these interactions with the aim to understand the role of aphid-host protein interactions in host susceptibility.

The student will use molecular biology and biochemistry approaches, such mutagenesis, Gateway cloning and co-immunoprecipitation assays, to validate protein-protein interactions. In addition, in planta functional assays will be used to explore the link between effector-host protein interactions and susceptibility. These assays will include in planta overexpression and silencing of host proteins as well as aphid effectors, and aphid performance assays.

The project will help us better understand how aphids are able to manipulate the host to their own benefit, and generate novel insight into the molecular co-evolution of plant-herbivorous insect interactions. Such insight will, in the longer term, underpin the development of novel sustainable pest control strategies.

Professor Miratul Muqit

Phosphorylation and ubiquitylation are reversible signalling events and there is significant interest in in their interplay in the regulation of normal biological processes and disruption in human diseases. Previous research in our lab has defined a role of the PINK1 kinase and Parkin ubiquitin ligase in sensing mitochondrial damage and eliminating damaged mitochondria by autophagy (mitophagy). How the pathway is regulated by other mitochondrial proteins is of interest. However, a major challenge in studying mitochondrial protein biology is that many mitochondrial proteins are essential limiting the ability to generate knockout cell types. The project will employ CRISPR/Cas9 genome editing technology and PROTAC approaches to chemically degrade candidate PINK1 regulator proteins. These studies will lead to greater understanding on how PINK1 is regulated that will be of relevance for Parkinson’s disease mechanisms.

Dr Peter Cossar

Proteins rarely function in isolation; instead, they form biomolecular complexes by interacting with other biomolecules, including DNA, RNA, and proteins. One such protein is TDP-43, an RNA-binding protein. In amyotrophic lateral sclerosis (ALS), TDP-43 is mislocalized to the cytosol, leading to protein aggregation and neurotoxicity. While advances in molecular cell biology have illuminated aspects of TDP-43’s role in ALS, its mislocalization remains poorly understood due to a lack of effective chemical tools that specifically target TDP-43. This Master’s project aims to develop molecular glues to restore TDP-43 localization to the nucleus, enabling studies on its role in ALS and supporting the development of a new drug modality.

In this joint Master’s project between the McGurk and Cossar Labs, you will integrate molecular biophysics, drug screening approaches, and structural biology to develop chemical tools that stabilize TDP-43 in a biomolecular complex. Specifically, you will:

Biophysically and structurally characterize TDP-43 in complex with its RNA substrate.
Identify and optimize drug-like chemical matter that targets protein-RNA and protein-protein complexes, and characterize their binding.
Investigate how small molecules mediate the relocalisation of TDP-43.

You will be based in the Cossar Lab within the Centre for Targeted Protein Degradation, a multidisciplinary environment with world-class facilities. This project will develop your expertise in molecular biophysics, organic chemistry, and chemical and structural biology. The lab employs molecular glue-, covalent-, and fragment-based drug discovery approaches to address fundamental molecular biology questions, providing a comprehensive training experience.

You will collaborate closely with the McGurk Lab within the Division of Cell and Developmental Biology. The McGurk Lab applies a range of techniques, including fruit fly genetics, in vitro biochemistry, and mammalian cell and neuronal culture systems, offering exposure to diverse biological methodologies.

Ideal applicants will have a strong interest in drug discovery and molecular biophysics. Prior experience in protein production or organic synthesis is preferred but not essential. The project can be tailored to your specific interests, and you will receive personalized mentorship to enhance your technical skills and professional development.

The University of Dundee’s inclusive research community offers an excellent setting for ambitious individuals. We welcome applications from all talented candidates, especially those with the drive and potential to make significant contributions to the field of drug discovery.

Chiara Maniaci

The Maniaci Lab tackles one of the big puzzles in cell biology: How can cells create a vast diversity of proteins from a limited genetic blueprint? This diversity is essential for life and is largely achieved through post-translational modifications (PTMs) – molecular “tags” added to proteins after they’re made. PTMs allow proteins to adopt different shapes, locations, and functions, enabling cells to adapt to changing conditions and perform complex tasks. However, when PTMs are improperly regulated, it can disrupt cellular balance, leading to diseases such as cancer and neurodegenerative disorders. Despite their importance, many PTMs remain unknown or poorly understood, and uncovering them could transform our understanding of health and disease.

In this project, we will explore an exciting new PTM mechanism that our lab recently discovered, known as “cleave-to-modify.” This pathway involves the strategic processing of proteins that contain ubiquitin-like domains, setting the stage for further modifications that allow precise control over protein functions. We aim to dissect this mechanism in detail, identifying the molecular players involved and understanding how they contribute to cellular regulation. By mapping out this pathway, we hope to uncover novel strategies for influencing protein behaviour, opening up new avenues for targeted therapies.

The potential impact of this project is far-reaching. By illuminating how cells manage protein diversity and function, this work could identify novel drug targets for treating diseases linked to PTM dysregulation. Imagine a future where we can precisely manipulate PTMs to halt cancer progression or counteract neurodegenerative damage – that’s the kind of possibility this project could unlock. For students, this is an opportunity to contribute to high-impact research at the cutting edge of cell biology and biomedical science.

Throughout this project, students will develop a strong skill set across biochemistry, cell biology, and quantitative proteomics, using a custom toolkit designed in our lab to study the ubiquitin-like fusion protein system. The project provides a unique hands-on learning experience, integrating method development with real-world applications in disease research. Students will work within an interdisciplinary team, gaining exposure to diverse scientific approaches and insights. This is an ideal project for those who are curious about how cells work at the molecular level, excited to develop new skills, and eager to be part of research that could ultimately impact human health.

Dr Ashleigh Holmes (based at James Hutton Institute)

Professor Nicola Stanley-Wall

Domestic crop production, increasingly reliant on reduced fertiliser and agrochemical inputs whilst also achieving high yields, is necessary to maintain a high level of food security in the UK. Increased demand for berries is driven both by their popularity and their proven health benefits. Like many crop and tree species, strawberries and raspberries are susceptible to diseases caused by oomycete pathogens, causing significant crop losses. Phytophthora root rot has reduced raspberry production by 80 % in the UK since the 1980s and growers now plant into substrate rather than directly into soil. The causal pathogen of root rot, Phytophthora rubi, can persist in the soil long-term and chemical control options are limited due to resistance. There is an urgent need to find more durable and sustainable methods of raspberry production. Understanding the underpinning mechanisms of biocontrol could lead to the identification of sustainable agri-chem products for the future. Preliminary data show that Bacillus spp can reduce P rubi growth in vitro and induce stress phenotypes in the pathogen, such as cell wall thickening and bulging.

The aim of this project is to examine the interactions between Phytophthora rubi and Bacillus spp with the goal of defining the molecular mechanisms involved in bacterial biocontrol of oomycete plant pathogens.

This project has four objectives:

Assess the genomes of Bacillus spp, for secondary metabolite biosynthetic gene clusters (BGC) using bioinformatics.
Investigate the transcriptome responses of Bacillus spp and Phytophthora rubi co-culture using RNA-seq methods.
Investigate Phytophthora-Bacillus interactions and impacts on raspberry roots, e.g. plant growth promotion by Bacillus or reduction in disease under oomycete challenge.
Functionally characterise Bacillus secondary metabolites involved in biocontrol of Phytophthora root rot.

The MRes project will provide the student with a foundation of skills in molecular microbiology, microscopy, plant cell biology, bioinformatics and knowledge exchange. This multidisciplinary approach will put the student in good stead for a successful postgraduate career. It will investigate the molecular mechanisms of bacterial biocontrol of an oomycete plant pathogen. The project would team Dr Ashleigh Holmes’ expertise on plant-microbe interactions with Prof Nicola Stanley-Wall’s fundamental knowledge of Bacillus biofilm formation and mixed-species communities. Bacteriology and stakeholder engagement advice will be provided by Dr Sonia Humphris (James Hutton Institute). The student will also engage with the Hutton soft fruit group with advice from plant production technicians and Phytophthora expertise in the wider Hutton plant pathology group. The project provides work experience in Institute and University based research environments. The student will have the opportunity to attend relevant postgraduate training courses at both Institutions, including access to BioSS statistical training modules.

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