DTP3 Cohort 4 Details
Lizzie Rank
Newcastle University
Supervisor: Dr Fiona Cuskin
Project Title: The role of bacterial exopolysacchairdes in the maintenance of healthy human gut bacteria.
Research Interests: The Bacteroides phyla are the main polysaccharide degraders found in the microbiome, targeting mainly dietary polysaccharides. Whilst many Bacteroides have been studied in terms of dietary polysaccharide breakdown, there is little biochemical data to describe how Bacteroides breakdown polysaccharides derived from other microbes.
My PhD project aims to assess the ability of human gut Bacteroides to degrade lactic acid bacteria exopolysaccharides. I will use growth studies, microbial community profiling, recombinant protein technology and biochemical analysis of degradation products and enzyme activity to elucidate the carbohydrate mediated relationship in the complex environment that is the human gut. This project will be in collaboration with Thermo Fisher Scientific.
Ellen Boswell
University of Liverpool
Supervisor: Professor Andy Jones
Project Title: Computational analyses of the conservation, competition and crosstalk of lysine-based post-translational modifications (PTMs)
Research Interests: Post-translational modifications (PTMs) (such as phosphorylation, methylation, ubiquitination and SUMOylation) modulate many biological processes and have also been linked to diseases such as cancer. Lysine is of particular importance since it is the amino acid which undergoes the most PTMs. This project will use computational methods to:
1. Re-process mass spectrometry data to produce PTM builds which will then be deposited in UniProtKB.
2. Study the competition and crosstalk between lysine modifications.
3. Investigate the evolutionary conservation of PTM relationships to help explain site-specificity rules.
The analyses will be carried out for humans as well as model organisms since PTMs may be conserved and thus any results may underpin ‘Rules of Life’. Ultimately, this work may help to elucidate possible mechanisms of disease for further study.
Chia Shyan Beh
Newcastle University
Supervisor: Prof. Majlinda Lako
Project Title: DRAM2: on the crossroad between trans-Golgi network and lysosomes?
Research Interests: Coming from a family of optometrists, I am intrigued by how vision is transmitted from the eye to make informed judgements. At university, I gained insights in areas of ophthalmology, regenerative medicine, visual neuroscience, genetics, clinical ageing, and translational medicine, which drives my passion. With research, I aim to enhance discovery and understanding of eye development across multiple organisms in hopes of addressing ocular diseases/visual conditions.
I am interested in this project which addresses a disease modelling approach to investigate molecular interactions in DRAM2 inherited retinal dystrophy. This project utilises different disease models to investigate retinal degeneration, a topic that I have in depth knowledge in. Via previous research projects, I recognised the milestones and limitations of the use of different models in retinal degenerative diseases, inspiring me to further my research into how molecular factors and disease models play a role in pathological presentations. I am intrigued by how defective systemic modifications and trafficking of proteins in the trans-Golgi network and lysosomal system cause death of specialized photoreceptors in the eye, ultimately leading to blindness. Upon successful understanding of such factors, this project offers clinical translation of such discoveries into new treatments/therapeutics to improve and enhance the ocular health of patients, a form of public engagement that I am eager to seek into.
Ana Constanza Hernandez Romero 
University of Liverpool
Supervisor: Dr Karl Bates
Project Title: Determining the impact of lifestyle-related biomechanics on muscle in the ageing human arm
Research Interests: This project aims to investigate the impact of habitual arm use on age-related changes in muscle architecture and function. State-of-the-art medical imaging will be utilized along with, image analysis, and biomechanical techniques to assess muscle architecture in two different cohorts: office workers and manual workers. By employing MRI scanning and deterministic fibre tractography, age-related variations will be measured in muscle architecture. The subjects will also undergo functional measurements related to forearm-hand muscle strength and movement precision. The relationship between muscle architecture and musculoskeletal performance will be also analyzed by exploring the hypothesis that inhomogeneity in fibre architecture is vital to normal muscle function in the forearm and hand.
Jude Ogunmola Oluwafemi
University of Liverpool
Supervisor: Professor Jane Hodgkinson
Project Title: Developing novel flukicides: the effect of neurotoxic spider venoms on the parasite, Fasciola hepatica
Research Interests: There is a threat to long-term control of the liver fluke parasite, Fasciola hepatica, due to widespread resistance to the most effective flukicide, triclabendazole. It has been shown that spider venom toxins, such as neurotoxins, affect insects' nervous systems specifically by acting on their ion channels. My research will explore the effects of novel neurotoxins derived from spider venom on liver flukes. Spider venom toxins (SVTs) have been hypothesized to act on liver fluke ion channels and have potential as next-generation flukicides. Therefore, my research will evaluate the potential of three neurotoxins and interrogate the mechanisms underlying their effects on F. hepatica. To accomplish this, the project will employ cutting-edge techniques like recombinant protein production, protein modeling, in vitro toxicity assays, imaging, and bioinformatics.
Linkedin: linkedin.com/in/oluwafemijudeogunmola
Twitter: @femijude
Amaya Malmalabaduge
University of Liverpool
Supervisor: Dr Natalia Sanchez-Soriano
Project Title: Investigating the connection between cytoskeletal and mitochondrial homeostasis during ageing
Research Interests: With increasing age, our neurons are at risk of damage, leading to the deterioration of sensory, motor and cognitive performance. Furthermore, ageing is the highest risk factor of multiple neurodegenerative diseases. Yet, we know too little about the mechanisms that drive processes of ageing and neuronal decay.
Previous studies conducted by my lab group and literature hypothesises a causative link between microtubule deterioration, altered organelle biology and the decay of axons and synapses that occurs during ageing. The aim of my PhD project is to assess the effect of ageing on mitochondria and establish whether and/or how microtubule deterioration provides a possible underlying mechanism and therapeutical avenue. I will be working with in vivo models of ageing, primarily the brain of the fruit fly Drosophila, as well as mammalian cell models and human cells from young and old individuals, to study the relevance of my findings and to increase the impact of my research.
Vincent Chriscoli
University of Liverpool
Supervisor: Luning Liu
Project Title: Molecular principles for the assembly and biogenesis of a-carboxysomes
Research Interests: I am currently interested in the carboxysome life cycle and the potential application of carboxysomes to various aspects of biology from disease treatment to improving crop yields for agriculture. My PhD project aims to understand the life cycle of an alpha carboxysome from biogenesis to degradation.
Safa Chogule
Durham University
Supervisor: Dr. Karrera Djoko
Project Title: A balancing act: how hosts control metal availability to their microbiota.
Research Interests: My PhD project aims to study the role of Histatins, a family of copper-binding salivary peptides, in governing the assembly, dynamics, stability and vulnernability of the oral microbiota.
The complexity of the oral microbiome is such that there is a selective need for nutritional immunity for local microbes and withheld for pathogenic microbes. With this project, we can analyze the importance of host-microbiome relationships based on metallo-protein interactions, in particular, studying the influence of nutrient copper availability.
Rosella Pinckney
Durham University
Supervisor: Dr Liz Morris
Project Title: Structure and mechanism of how phages modulate bacterial immunity
Research Interests: I have an MSci in Natural Sciences (Biology and Chemistry) from Durham University. During my master’s project I studied Zika virus’ non-structural 3 protein helicase domain. I enjoyed utilising my background in Biology and Chemistry to study the protein and its interactions with small molecules; using techniques such as activity-based protein profiling and thermal shift assays. I am interested in using biophysical techniques to study proteins structure and function in order to accelerate drug discovery. I enjoy learning about viral proteins and their mechanisms; gaining an understanding of this can aid in developing new treatments for diseases. This project will allow me to use techniques such as X-ray crystallography and cryoEM and explore phage therapy as an alternative to antibiotics.
George Parsons
Newcastle University
Supervisor: Dr Catriona Anderson
Project Title: Exploring the role of vitamin transport in insect models of disease vector biology
Research Interests: Sap-feeding and blood-feeding arthropods (such as aphids and bedbugs) supplement their vitamin-lacking diets through partnerships with microbial symbionts, exchanging nutrients across the multiple membranes that separate the arthropod gut from the bacterial cytoplasm.
The positions of nutrients between these membranes have been described yet the transporter proteins responsible for moving them across remain broadly unknown.
My research will identify, locate, and characterise these transporters using RNA sequencing, immunocytochemistry, and functional assays, with the aim of providing targets for the future development of highly specific pesticides to inhibit these proteins helping to protect crops and mitigate the spread of vector-borne diseases in humans.
Cameron Read
Newcastle University
Supervisor: Dr Toby Hallam
Project Title: Large-scale Integration of Microfluidic IntigraTed Sensors (LIMITS)
Research Interests: My research interests and PhD will focus on the development of a microfluidic system to detect biological contamination in waterways and marine environments. Effective water quality testing is not only important for water companies and regulators but also for individuals who care about the natural environment and public health. My research will deliver a proof-of-concept testing system that is able to carry out automated, longitudinal biological testing for markers of fecal contamination such as E. coli in in waterways. This will require an interdisciplinary approach, combing my knowledge of manufacturing 3D printed microfluidics with integrating electrodes, following this will be biologically functionalisation of the sensors including cell capturing and sensing. The final stage of my research will focus on signal analysis, packaging of electronics and design improvements before conducting field tests and verification.
Geethanjali Thenissery Veedu
Newcastle University
Supervisor: Dr Claudia Schneider
Project Title: How does the nucleolus safeguard ribosome production during meiosis?
Research Interests: I am broadly interested in gene regulation, chromatin biology and developmental biology
Ranjit Rai
Durham University
Supervisor: Professor Martin Goldberg
Project Title: Stress and aging in the nuclear pore complex and associated cytoskeleton: a 3D super-resolution light and electron microscopy study
Research Interests: The nuclear pore complex (NPC) is the gateway into and out of the nucleus. NPCs are key for maintaining cellular homeostasis by maintaining a barrier function, but during ageing and physical/chemical stresses, NPCs can become inefficient and leaky, upsetting cellular homeostasis and leading to pathologies. For my PhD I will be using C.elegans intestine as a model system to assess the effects of stress and aging on the NPC and its interactions with the cytoskeleton. During this project, I will be using super resolution light microscopy techniques of live and fixed worms, 2D electron microscopy (EM) and 3D volume EM to assess the structural organisation of NPCs and cytoskeleton throughout the intestine, and how this is disrupted during stress and aging.
Meihan Meng
Newcastle University
Supervisor: Prof. Matthias Trost
Project Title: Characterising the role of ubiquitylation in endo-lysosomal trafficking by highly
sensitive ion mobility mass spectrometry
Research Interests: The phagocytosis of ‘foreign bodies’ is one of the major pillars of the innate immune system. Microbes engulfed by phagocytosis are delivered into an intracellular organelle called phagosome. The increasing evidence indicated that ubiquitylation of phagosomal proteins may play an important, yet undiscovered, role in the phago-lysosomal system. Therefore, my PhD project will be to study how ubiquitylation affects phagosome maturation at the molecular level. In achieving this, I will be using sophisticated tools for the isolation of silica bead-induced phagosomes, followed by the purification of ubiquitin-containing proteins. In addition to biochemical assays and molecular biology approaches, such as flow cytometry and immunofluorescence microscopy, I will apply proteomics together to characterise the roles of atypical ubiquitin chain types in phagosome biology. I will also have a great opportunity to collaborate with Bruker Daltonics, a leading mass spectrometry company, to utilise state-of-the-art TIMS-ToF mass spectrometry. Findings will help us better understand how post-translational modifications regulate the phago-lysosomal system.
Kathleen Bialik
Newcastle University
Supervisor: Jon Marles-Wright
Project Title: Structural and Biochemical Understanding of Bacterial Ceramide Synthesis
Research Interests:
Using microbiological and biochemical analysis, this project seeks to deepen our understanding of the bacterial ceramide synthesis pathway and investigate the role of sphingolipids in selected bacterial species of different niches including those of the gut-microbiome, oral cavity, soil, and water. The bacterial ceramide synthesis pathway has not yet been characterised. This project will use structural and biochemical methods combined with molecular microbiology to understand the function of key enzymes in this pathway. The pathway has a dedicated acyl-carrier protein that is responsible for delivering acyl-chains to the serine-palmitoyl transferase enzyme, which catalyses the first committed step in this pathway. I will characterise the interaction between these two proteins using X-ray crystallography and biophysical methods. The bacterial ceramide synthase enzyme (bCerS) is distinct from the membrane-bound eukaryotic ceramide synthases, in which structure have recently been published, and thus is the primary interest of my project. I will perform a full biochemical and structural analysis of this protein to understand its activity and substrate specificity. In final aim of the project, I will perform phenotypic studies to understand the role of bacterial ceramides in host microbe interactions. This project combines my passion for microbiology as well as utilizing a variety of techniques including protein purification, microscopy, biochemical assays, animal models and more.
Huei Teng Ng
University of Liverpool
Supervisor: Dr Bettina Wilm
Project Title: Developing novel technologies to analyse cellular differentiation processes during embryonic development in vivo and ex vivo.
Research Interests: Mesothelial cells are crucial in maintaining serosal homeostasis. It forms a non-adhesive protective monolayer to allow movement of our internal organs and has the ability to regenerate after injuries. Previous studies employing genetic lineage tracing methods have shown mesothelial cells contributed to formation of vasculature smooth muscle cell (vSMC) in mouse embryo. However, the exact time and process of how mesothelial cells specialised into of vSMC is still remained unknown. Therefore, the aim of this project is to determine the differentiation processes of vSMC originating from mesothelial cells. This project will incorporate a new tissue culture technique called Gastruloids to represent early stage of embryo formation and 3D electron microscopy to characterise vSMC.
Ross McDonagh
Newcastle University
Supervisor: Prof. Chris Dennison
Project Title: How does metal binding affect the function of proteins targeted by a
devastating pathogen of cereal crops?
Research Interests: My project will be conducted in the field of Biological Chemistry, with a specific focus on protein-metal binding. My passion for structural biology has been a driving force throughout my academic journey, from my BSc in Chemistry to my MSc in Protein Chemistry at the University of Galway, Ireland.
My research will aim to highlight the significance of protein-metal binding in rice heavy-metal-associated plant proteins (HPPs), including heavy-metal-associated isoprenylated plant proteins (HIPPs), in their function and their role in pathogensis. These proteins are targeted by effector proteins from Magnaporthe oryzae, a pathogen which contributes to a significant reduction in rice yield. By studying these interactions, I hope to aid in the understanding of how this pathogen-induced crop failure can be prevented, ultimately reducing food scarcity issues.
Joel Doherty
University of Liverpool
Supervisor: Dr Howbeer Muhamad Ali
Project Title: Application of molecular imaging techniques for better understanding antimicrobial resistance in biofilms.
Research Interests: Microbiology. Namely understanding and combating antimicrobial resistance in bacterial communities through the application of computational methods and wet-lab research. My project will utilise state-of-the-art metabolomics approaches to monitor changes in metabolic profiles, and the response of bacterial cells in biofilms, upon exposure to various antimicrobial treatments.
LinkedIn: https://www.linkedin.com/in/joel-doherty/
George Weston
Durham University
Supervisor: Prof. Martin Cann
Project Title: A Machine Learning Approach to Identify Carbon Dioxide-Binding Proteins for Sustainability and Health
Research Interests: Carbon dioxide has a fundamental role in biological processes throughout the biosphere. While a huge amount is known about the impact of the gas in physiology, little is known about CO2 targets on proteins. This research aims to build on previous work which used triethyloxonium ions to trap carbamates on proteins enabling their identification by tandem mass spectroscopy. A machine-learning approach will be produced (called the Global Carbamate Predictor, GCarP) which aims to predict CO2-binding sites on proteins by using information about the lysine structure, dynamics and the local environment.
Sophie Park
University of Liverpool
Supervisor: Dr John Graham-Brown
Project Title: Improving sustainable parasite control in British dairy cattle
Research Interests: I am highly interested in researching health and disease, particularly parasites, in ruminant species.
Eirini Tafanidou
Newcastle University
Supervisor: Professor David Elliott
Project Title: Analysis how de novo mutations in an RNA splicing regulator change global gene
expression patterns.
Research Interests: My project aims to understand how RBM5, an RNA splicing regulator can cause male infertility. Specifically, I aim to understand how point mutations in RBM5 affect its function in regulating gene expression in cells.
Sara Ilic
Newcastle University
Supervisor: Elizabeth Veal
Project Title: How does the ability of Peroxiredoxins to form complexes affect cell-protective responses to reactive oxygen species (ROS)?
Research Interests: My research interests revolve around immunology, protein-based research, pharmacology and therapeutics.
My project looks into Reactive oxygen species (ROS). ROS cause oxidative damage, which makes major contributions to disease. However, ROS also have important, signalling functions; initiating responses that maintain cell viability/organismal health. Peroxiredoxins (Prdx) are peroxide-sensing proteins which are important for ROS signal transduction. Prdx oligomerise but also form ROS-induced disulphide complexes with other proteins, including P38 mitogen activated protein kinase (MAPK) signalling proteins. The overall aim of this project is to establish the role that peroxiredoxin (Prdx) complexes play in regulating specific ROS-signalling outputs, protein homeostasis and ageing. With the ultimate goal being to investigate whether conditions that specifically promote or block Prdx oligomerisation have therapeutic potential as modulators of aging or age-associated diseases, including cancer.
Bartosz Witek
Newcastle University
Supervisor: Maxim Kapralov and Leonardo Rios
Project Title: Engineering and de novo design of CO2 metabolism in engineered microbial consortia as the next generation platform to produce high value chemicals
Research Interests: Photosynthesis can be engineered to use the harnessed solar light energy to sustainable create industrially important feedstocks and high-value products from carbon dioxide fixation. However, engineering photosynthetic organisms for such purposes has proved challenging. We aim to overcome these limitations by coupling the awesome photosynthetic power of cyanobacteria with engineered yeast strains to power high-value product synthesis, within synthetic microbial consortia. Further, we will try to introduce carbon dioxide fixation mechanisms in yeast and other heterotrophs to try to directly couple capture of carbon dioxide from the atmosphere to product synthesis.
Alistair Topping
University of Liverpool
Supervisor: Dr Vanja Pekovic-Vaughan
Project Title: Targeting Neuromuscular Ageing using Novel Synthetic Retinoids and Chrono-Pharmacological Approaches
Research Interests: My PhD project is a CASE project, and I will be working with Nevrargenics, a company which has developed a suite of novel synthetic retinoid analogues, which are currently under investigation for applications in neurodegenerative diseases.
Our preliminary data shows that application of retinoids majorly affects circadian rhythms, and that the retinoic acid signalling system is subject to time of day-based expression. We aim to find the interlink between these two signalling pathways and determine exact molecular mechanism underlying these findings.
We will also be utilising chrono-pharmacological approaches to determine if the toxicity profile of these drugs can be altered depending on the time of day of their application.
Katherine Convey
Newcastle University
Supervisor: Thomas Howard
Project Title: Smart Materials for Equipment-Free Surveillance of Plant Viruses
Research Interests: My research focus lies in addressing the critical challenge of ensuring food security amidst a changing global climate and the escalating threat of pathogen-related diseases in agriculture. I am particularly interested in the significant impact of plant viruses, which not only cause substantial economic losses worldwide but also pose a direct threat to the stability of our global food supply. My upcoming PhD project aims to enhance in-field diagnostics through real-time monitoring of viral infections in crop plants, utilizing the exciting potential of cell-free synthetic biology methodologies. By harnessing the power of these cell-free approaches, I aim to help develop a versatile, portable, on-site testing system capable of promptly detecting and distinguishing between damaging plant viruses. This approach holds the potential revolutionize disease surveillance and containment strategies, ultimately culminating in a practical technology that empowers agricultural stakeholders to effectively mitigate viral risks and safeguard food crop production.
I am excited about the potential of translating scientific research into sustainable technologies with real-world impact, and I am eager to continue addressing environmental challenges through innovative approaches in biotechnology in my future career.
Lewis Isaac Chan
Newcastle University
Supervisor: Sergey Melnikov
Project Title: Power naps: ribosome hibernation as a booster of antimicrobial resistance
Research Interests: Translation, antimicrobial resistance, evolution, drug-binding, microbiology, cryo-electron microscopy.