Teaching and assessment for Life Sciences Masters by Research MSc (Res)
Teaching
You'll be taught through a mix of:
- supervised laboratory research
- workshops
- induction programme for postgraduate research
- poster presentation
- super seminars
- journal clubs
Alongside basic science training in experimental design, data handling, and research ethics, we will help you develop skills in critical assessment and communication.
Your research will be supported by workshops in scientific writing, presentation skills, ethics, laboratory safety, statistics, public engagement and optional applied bioinformatics.
Assessment
You'll be assessed through
- a written thesis
- with oral examination at the discretion of the examiners
Projects
You’ll select a research project from the following options, design and undertake research, before writing up your findings in the form of a thesis. You will need to list your top three project choices as part of your application.
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.
Recent advances from the Ciulli Lab and others have contributed to the establishment of a game-changing 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 signaling 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. Our science takes advantage of latest technologies and vast expertise available within our newly opened Centre for Targeted Protein Degradation (CeTPD) and within the wider School of Life Sciences e.g. the FingerPrint Proteomics and Cryo-EM Facilities. We collaborate with several research groups within the School, including the Divisions of MRC-PPU, MCDB and CSI, amongst others, to deploy our molecules to interrogate the biology of targets of interest and to dissect the functional consequences of selectively disrupting or augmenting the signaling networks in which they are involved.
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. 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 (a.ciulli@dundee.ac.uk).
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.
An intramolecular bivalent degrader glues an intrinsic BRD4-DCAF16 interaction
bioRxiv 2023.02.14.528511; doi: https://doi.org/10.1101/2023.02.14.528511
Ramachandran, S. et al.
Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2
ChemRxiv Cambridge: Cambridge Open Engage; 2022; DOI: 10.26434/chemrxiv-2022-bvj80 (In Press at Nat. Commun.)
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.
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.
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.
Lignin is a major component of plant cell walls, and has a significant influence on the digestibility and uses of plant biomass. The lignin biosynthesis pathway has been one of the most intensively studied plant metabolic pathways over the past two decades.
Nevertheless several fundamental aspects of lignification remain to be understood including aspects of its regulation and its developmental coordination with wider plant metabolism. These are important questions to address given the current world-wide focus on the bio-economy, and the potential of using plant biomass as a renewable feedstock to displace the use of fossil resources and reduce carbon dioxide emissions. We have been using Genome Wide Association Studies (GWAS) across a panel of elite barley cultivars to identify the loci and genes that influence lignin biosynthesis and straw digestibility. We have identified many exciting candidate genes and, in the process, have uncovered networks of interacting genes that cooperate to produce plant secondary cell walls and ensure the production of strong stems that support high grain yield. The networks include many genes of unknown function or that are not appreciated to be involved in cell wall development and we want to discover their specific roles and functions. Some are transcription factors of various classes and others are biosynthetic enzymes. This Masters by Research will help to elucidate how these gene networks function by investigating the roles of a few specific genes. We have large datasets that will facilitate the work including large populations of cultivars with RNAseq and exome capture data (providing gene expression levels in different tissues plus information on single nucleotide polymorphisms –SNPs), a pseudomolecule assembly of the barley genome, TILLING populations of barley mutants, and the ability to use very efficient transgenesis methods (RNAi and CRISPR). Understanding how these genes interact and how they influence cell wall traits will produce data both of fundament importance to understanding plant biology, and of translational importance in expanding opportunities for targeted improvement of plant biomass by rational ‘designer’ approaches. This project can be adapted to the interests of candidates, and, depending on the specifics of the project developed, provides opportunities fortraining in a wide range molecular techniques, in bioinformatics, in biochemistry and cell biology, and/or in the production of gene edited or RNAi transgenic plants. The student will be part of the University of Dundee, School of Life Sciences but will be based In the Division of Plant Sciences at the near-by James Hutton Institute and will benefit from the facilities and expertise on both sites.
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.
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 (tly@dundee.ac.uk).
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?
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 tumors 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.
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.
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
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 ablicans, 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
Many important processes within mammalian cells are compartmentalised within specific subcellular structures. In the cell nucleus, Nuclear Bodies (NBs), such as nucleoli, provide specialised compartments that are not surrounded by membranes, but still concentrate specific proteins and RNAs. The number and morphology of NBs varies according to cell type, cell physiology and growth state. NBs are also frequently altered in cells with mutations causing inherited genetic disorders and change when cells respond to stress, or disease mechanisms, including viral infection and cancer. NBs can assemble and disassemble, both in interphase and during mitosis, and their component molecules continually traffic through them. Therefore, the appearance of NBs detected by microscopy represents a steady state image of dynamic structures. Importantly, the size, morphology and molecular composition of NBs can rapidly change in response to perturbations and variation in the cell environment.
Despite the major functional importance and clinical relevance of the processes of ribosome subunit biogenesis and pre-mRNA splicing, we still lack a detailed understanding of how these processes take place within the cell nucleus, including how the assembly of both the rRNA and pre-mRNA processing machineries are compartmentalised within the different NB structures that are detected by microscopy.
This project is designed to improve our mechanistic understanding of these important structure-function relationships in the cell nucleus. We have identified small molecule chemical tools, which we term, ‘NB modulators’ (NBMs), that alter the structure and composition of specific NBs, including nucleoli, speckles and CBs. We will use these chemical modulators, in conjunction with high resolution electron microscopy, light microscopy and poly-omics assays, to characterise in detail how the structures and properties of NBs are affected by NBMs.
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
The overarching goal of our research is to identify and characterise the protein kinase signalling pathways that control stem cell pluripotency and differentiation and determine how protein kinase signalling is disrupted to cause human developmental 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 pluripotent stem cells (PSCs) into adult tissues, such as neurons, cardiomyocytes and hepatocytes. Furthermore, protein kinase signalling pathways are frequently dysregulated in human diseases and developmental 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 in PSCs. However, beyond several notable examples, protein kinase pathways, regulatory mechanisms and molecular functions that control of pluripotent stem cell maintenance and differentiation remain poorly understood.
Ser-Arg Rich Splicing Factor (SRSF) 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 genetic programmes required for development, whilst SRPK-RNF12 pathway components are disrupted in a series of related human developmental disorders. These data suggest that SRPK plays a key role in PSC maintenance and development, and that dysregulated SRPK signalling may underpin human developmental disorders.
The goal of this project is to investigate the regulation and function of novel SRPK substrates our lab has recently identified by state-of-the-art global phosphoprotemic profiling. The aim of the project is to explore mechanisms by which SRPK phosphorylation regulates substrates and define their functions in regulation of downstream biological processes in PSCs and differentiating neurons. Finally, they will determine whether and how the SRPK signalling pathway is disrupted in patients will neurodevelopmental disorders. This project offers a unique opportunity to illuminate new molecular mechanisms underpinning PSC regulation and their dysregulation in human disease.
Selected recent work from the lab can be found in the following references (Findlay lab members in italics):
- Bustos, F., Segarra-Fas, A., Nardocci, G., Cassidy, A., Antico, O., Brandenburg, L., Macartney, T., Toth, R., Hastie, C.J., Gourlay, R., Vargese, J., Soares, R., Montecino, M. and Findlay, G.M. (2020) Functional diversification of SRSF protein kinase to control ubiquitin- dependent neurodevelopmental signalling. Dev Cell. 55(5):629-647
- Fernandez-Alonso, R., Bustos, F., Budzyk, M., Kumar, P., Helbig, A.O., Hukelmann, J., Lamond, A.I., Lanner, F., Zhou, H., Petsalaki, E. and Findlay, G.M. (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
- Bustos, F.*, Segarra-Fas, A.*, Chaugule, V.K., Brandenburg, L., Branigan, E., Toth, R., Macartney, T., Knebel, A., Hay, R.T., Walden, H. and Findlay, G.M. (2018) RNF12 X- linked intellectual disability mutations disrupt E3 ligase activity and neural differentiation. Cell Rep. 23(6): 1599-1611
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 dhmurray@dundee.ac.uk or by visiting our website. https://sites.dundee.ac.uk/david-murray-lab/
Plant architecture, or body plan, plays a key role in determining grain yield of crop plants. However, we have little understanding of the molecular genetic basis of architecture in the temperate cereals such as barley (Hordeum vulgare L.), especially in comparison to the warm weather crops such as rice (Oryza sativa). In my research group, we work with a family of genes which control agronomic traits in barley. In this project, the student will investigate how these genes work by studying alleles, or variants of these genes which change barley growth and development. The student will use state of the art genetic, molecular and genomic approaches and receive training in the latest crop bioinformatics. Through their work, the student will advance our understanding about how crops grow and develop and reveal possible routes to improved yield and greater resiliency. The student will train within the unique environment offered by the Division of Plant Sciences, based at the James Hutton Institute (JHI), a centre of world-class expertise in barley.
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 contribute to improved 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 that may control epidermal development in cereals1. 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.
1Liu 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
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. This involves the transport of proteasome assembly chaperone (PAC) mRNAs along actin structures and their relocalisation to a specific subcellular localisation upon stress to stimulate their translation. The goal of this project is to define how actin remodelling controls PAC mRNA translation and cell survival using budding yeast. The project will offer training opportunities in state-of-the-art technologies such as live-cell mRNA tracking using confocal microscopy, mRNA pull-down followed by proteomics and CRISPR/Cas9 genome editing.
Cereal grain provides more calories than any other source to our diet, making grain production vital to food security. We study grain development in barley, a globally important cereal, and a powerful genetic model system. Calories from grain mostly come from the starchy endosperm, which develops surrounded by nutritive and protective maternal tissues of the grain.
Our recent work suggests that growth and survival of maternal tissues is carefully balanced with the need for nutrients and space for the endosperm1, but the exact mechanism remains unclear. This project will use advanced methods in genetics, genomics and molecular biology to identify and characterise key genes that control maternal tissue development. The student will exploit cutting-edge transcriptomic approaches to understand how these key genes control gene expression during grain development.
This project would best suit a student fascinated by development and motivated to work on cereal improvement. The student will receive training in modern cereal genetics and as well as advanced bioinformatic skills. The McKim lab is a dynamic, productive and supportive research group located at the James Hutton Institute (JHI), a global leader in cereal genomics, and part of the International Barley Hub, a £62 million investment in cereal research. This student will benefit from training offered both by University of Dundee and JHI. We warmly welcome students from diverse backgrounds and cultures. Interested students are encouraged to contact me to discuss any aspects of the project. 1Shoesmith et al (2021) Development 148 (5): dev194894.
Post-translational modifications (PTMs) of proteins, such as ubiquitylation and phosphorylation, are fundamental determinants of protein function and cellular signalling. Misregulated PTMs are hallmarks of many human diseases, including cancer and neurodegeneration. In the Sapkota lab, we have developed new technologies that can alter specific PTMs on target proteins in cells. For example, by using the affinity-directed protein missile system, we can target specific proteins for degradation. Similarly, we can utilise the AdPhosphatase system for targeted dephosphorylation of phospho-proteins. This project seeks to explore targeted post-translational modifications of disease-relevant proteins to alter their function in cells in a desired manner. The student will be exposed to a blend of state-of-the-art biochemical, proteomics, and cell and molecular biology techniques, including the CRISPR/Cas9 genome editing technology.
Gastrulation is an essential process in early development, during which the forming ectoderm, mesoderm and endoderm take up their correct positions in the embryo. We investigate the how a few key cell behaviours mediate gastrulation in the early chick embryo, a widely used model for early human embryonic development. Gastrulation requires a precise coordination of cell division, cell differentiation, ingression and cell movement [1]. We study how these key cell behaviours are controlled by mechanical and chemical cell-cell signalling. To study these cell behaviours in-vivo we have developed a dedicated lightsheet microscope that allows us to see all cells in embryos of transgenic chick lines where components of the actin myosin cytoskeleton and nuclei are labelled with different fluorescent proteins. We locally or globally perturb chemical and mechanical signalling pathways that alter critical cell behaviours and study the effects on gastrulation [2, 3]. In this project we aim to analyse the detailed patterns of cell divisions during early development and through specific perturbations investigate the roles they play in the control of embryonic tissue development and morphogenesis. Our research is highly interdisciplinary, besides state of the art cellular and molecular biology approaches we make extensive use of advanced large scale computational (some AI based) image processing as well as modelling techniques [4]. Therefore, this project will offer the opportunity to perform research in a highly competitive, interdisciplinary environment.
- Serrano Najera, G. and C.J. Weijer, Cellular processes driving gastrulation in the avian embryo. Mech Dev, 2020. 163: p. 103624.
- Rozbicki, E., et al., Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation. Nat Cell Biol, 2015. 17(4): p. 397-408.
- Manli Chuai et al. Reconstruction of distinct vertebrate gastrulation modes via modulation of key cell behaviours in the chick embryo, 2023. Sci. Adv.9, eabn5429 (2023). DOI:10.1126/sciadv.abn5429
- Serra, M., et al., Dynamic morphoskeletons in development. Proc Natl Acad Sci U S A, 2020. 117(21): p. 11444-11449.
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.
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.
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 (pahemsley@dundee.ac.uk) before submitting an application.
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 (pahemsley@dundee.ac.uk) before submitting an application.
Ubiquitin is a small, yet influential, protein that is attached to other substrates to control their stability or activity in a process called ubiquitylation. Ubiquitylation underpins many biological pathways and is fundamental in maintaining cellular homeostasis. Ageing and environmental or genetic insults that disrupt the ubiquitylation process often lead to the development of debilitating human diseases (cancer, neurodegeneration, immunity disorders). E2 conjugating enzymes (E2s) play a pivotal role in the enzymatic cascade culminating in ubiquitin's attachment to a substrate. Traditionally perceived as a post-translational modification targeting lysine side chains and protein N-termini (canonical ubiquitylation), recent discoveries in the De Cesare lab spotlight E2s capable of conjugating ubiquitin to serine and/or threonine residues (non-canonical E2s). This type of ubiquitylation has been recently found to have larger and more pervasive roles than previously appreciated. In particular, the targeted disruption of non-canonical E2s in a mouse model has been found to have pleiotropic effects on fertility: it is crucial for the implantation and development of embryos and their subsequent viability during pregnancy. Comprehending the molecular mechanisms governing the attachment of healthy embryos to the uterus holds paramount importance in reproductive medicine. Our research utilizes various methodologies—quantitative proteomics, MALDI-TOF Mass Spectrometry, protein modeling and prediction tools alongside biochemical assays (SDS-PAGE, Western blotting, etc.)—to characterize non-canonical E2s. Additionally, we employ genetic and molecular biology techniques (including CRISPR-Cas9 for generating knock-out and knock-in cell lines, TAG degraders) to elucidate the intricate molecular pathways driving such a profound phenotype.
As a one-year Master's student, your involvement in our ongoing project will primarily be in the wet lab and can be tailored to align with your specific interests and motivations. If you are interested in contributing to the exploration of this new and exciting area of research, do not hesitate to get in touch with Virginia (Vdecesare@dundee.ac.uk – more information on https://www.ppu.mrc.ac.uk/research/principal-investigator/virginia-de-cesare).
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.
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.
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.
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.
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.
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.
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:
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 centers 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.
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, you 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. You will use a collection of B. subtilis and closely related species, for which genome sequence data is available. You 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.
The biological complexity observed in living organisms greatly exceeds the number of different forms of proteins (the proteome) that the encoding genomes would predict. One route of diversification that the cell uses to expand its proteome is via the covalent posttranslational modification (PTM) of proteins at one or more sites, allowing for the generation of new and different proteoforms. PTMs play a key role in many fundamental processes and the proper regulation of protein PTMs is critical for the correct functioning of the cell. When this process goes awry, it can lead to diseases such as cancer or neurodegeneration. Although some PTMs have been already characterized, many still remain to be identified and understood.
The major focus of the Maniaci Lab is to discover the fundamental principles of how cells expand the diversity of their proteome via previously unrecognised “cleave-to-modify” mechanism that we have recently uncovered. This mechanism involves the processing of Ubiquitin-like-domain containing proteins to enable their further modification as a means to regulate protein biological function. This project aims to characterize this previously unexplored mechanism in more detail and discover the key players involved in its regulation.
By uncovering the role and extent of this unprecedented mechanism, the proposed project will transform our understanding of protein processing and modification and, consequently, reveal new potential targets for pharmacological intervention.
The project merges several disciplines, ranging from method development, biochemistry, cell biology and quantitative proteomics and takes advantage of a recently developed toolkit to study the ubiquitin-like-fusion protein system. The project also complements ongoing lab efforts and expands upon our recent discoveries in this area.
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.
Immune activation triggers dramatic proteome remodelling. Using high sensitivity mass spectrometry we have mapped immune cell proteomes, providing novel insights into immune cell phenotypes and revealing the metabolic and protein synthesis machinery and environmental sensors that shape cell fate. However, our analysis has provided little insight into the subcellular dynamics of the immune cell proteome. The location of proteins to specific cellular compartments, and their movement between compartments, is essential for core cellular activities. Indeed, mis-localisation of proteins within the cell is linked to a range of diseases. This project aims to develop novel tools to explore the subcellular proteome of lymphocytes. These tools will be valuable for understanding how protein localisation is impacted by immune activation or by the modulation of key signalling pathways.
The project will provide the opportunity to master cutting edge skills in protein biochemistry and mass spectrometry and will generate new mechanistic insights into the activity of immune cells.
Microglia are constantly sensing the brain environment for metabolic changes, damage and pathogenic invasion. Microglia are highly metabolically active, with activation in response to inflammatory stimulation increasing glycolytic demand. Changes in nutrient availability, as a result of hypoglycaemia for example, lead to metabolic reprogramming of microglia via utilisation of glutamine and fatty acids to maintain their functional responses. Hyperglycaemia, as a result of poorly controlled diabetes, is associated with increased inflammation and risk of Alzheimer’s Disease. It is unclear however, how changes in nutrient availability alter microglia inflammatory responses and proteomic reprogramming. This project therefore aims to understand how key metabolic nutrients, glucose and glutamine, regulate microglia responses and metabolic/ proteomic reprogramming, specifically in response to protein aggregates and inflammatory cytokines associated with Alzheimer’s Disease.
This project will firstly seek to understand the rate of glucose and glutamine uptake in primary mouse microglia using fluorescent-labelled uptake assays under both homeostatic conditions and in response to the inflammatory stimulus lipopolysaccharide (LPS). These experiments will measure the changes in metabolic demand of microglia exposed to inflammatory stimuli over time.
Secondly, to understand how these metabolites are utilised in the proteome in homeostasis and inflammatory conditions, we will establish 13C metabolite tracing in microglia by culturing cells with 13C-labelled glucose and glutamine and performing mass spectrometry analysis. This will enable detailed mapping of intracellular nutrient utilisation by microglia.
Finally, to understand the extent of proteomic reprogramming and functional analysis, we will generate detailed proteomes of microglia under homeostatic and inflammatory conditions in media deprived of/ in hyperabundance of glucose and glutamine. This will allow us to analyse and quantify changes in the inflammatory landscape of microglia due to changes in nutrient abundance. We will then assess nutrient-dependent functional microglia changes using the zymosan phagocytosis assay.
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.
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