Pancreatic ductal adenocarcinoma (PDAC) is characterised by a stiff tumour environment and has no curative therapies. This stiff environment is produced by inappropriate deposition of components, known as the extracellular matrix, that are normally tightly regulated to support pancreatic cells. Despite the emergence of novel targeted therapies, chemoresistance continues to arise. Hence, we hypothesise the increased stiffness of PDAC tumours induces resistance to chemotherapy. By modelling the stiffness of healthy and diseased pancreas using polyacrylamide gels, my project will uncover how pancreatic cancer cell signalling is altered as a product of matrix stiffness, and how changes to the cell cycle and DNA damage response allow cells to escape chemotherapy. Preliminary evidence suggests PDAC cells grow better on stiffer gels and are more resistant to chemotherapy than on softer gels. Thus, harnessing the mechanisms underlying these pathways may allow us to bolster treatment efficacy.
AAA+ ATPases hydrolyze ATP to generate mechanical force used to disassemble macromolecular assemblies, which function for diverse cellular processes. We are interested in understanding how the activity of these AAA+ ATPase is regulated by post-translational modifications, which remains largely unknown. We focus on VPS4, a member of the meiotic clade of AAA+ ATPases family, is crucial for disassembling the membrane-remodelling ESCRT-III protein polymers, facilitating endosomal sorting of transmembrane receptors, organelle membrane repair and completing cell division. We explore how phosphorylation in the linker that joins substrate-binding and ATPase domain impact on the structure and activity of the enzyme. The unstructured linker sequence contains several identified phosphosites, some of which appear conserved. Using phosphomimetic mutants, we examine how modifications in the linker affects VPS4 activity in vitro and at cellular membranes.
The study of regenerative biology aims to understand how organisms naturally replace injured cells and tissues. Zebrafish larvae having excellent regenerative ability can be used as a model to study cellular and molecular aspects of regeneration. My project aims to understand how wound signals are able to activate the redevelopment of tissues during larval tail regeneration. Two signalling pathways (Hedgehog (HH) and transforming growth factor-β (TGF-β)) play a crucial role in larval regeneration. If either pathway is inhibited, regenerative cells are not recruited to the injured site. However, the detailed links between signals are poorly understood. My data supports the model that after tail excision TGF-β is induced by HH along with reactive oxygen species (ROS) which is produced at the wound site. The TGF-β then inhibits HH expression as part of a negative feedback loop. We hope that in the long term our research may aid in the development of new therapies in regenerative medicine.
Perovskite materials have significant potential for next-gen optoelectronics, due to their excellent optoelectronic properties and tuneable band gap. Due to the fabrication routes employed for these semiconductors, heterogeneities are introduced on multiple length scales. These have been shown to influence the stability of perovskite optoelectronic devices. Understanding heterogeneity on multiple length scales is critical to understanding the links between structure and device instability. In this work we use Kelvin Probe Force Microscopy (KPFM) to image the charge transport mechanisms of perovskite thin films with relation to their topography. This allows us to develop a picture of heterogeneity at the nano-scale which we then correlate with the chemistry of our materials. The results provide valuable insights into charge dynamics and give a promising indication of how KPFM can be utilised as a characterisation technique in the field.
Avian population declines arising from eggshell thinning induced by chemical exposure is now typically regarded as an historical threat. Evidence has started to emerge, however, that a wide range of pollutants are abundant in the environment that could generate eggshell thinning. These include historical ‘legacy’ pollutants and more novel emergent pollutants. Using a systematic literature review approach we provide an assessment of the potential for six main chemical groups, those being DDT and its metabolites, PCBs, PBDEs, PFASs, NSAIDs and neonicotinoid pesticides, to induce eggshell thinning. Assessment of the quantity and quality of evidence highlight that whilst much additional research is needed a number of these pollutants, in addition to DDT, have potential to induce avian eggshell thinning – with potential demographic consequences.
It is widely accepted that human activity is causing biodiversity loss globally. Zoos are well-placed in society to build connections between their visitors and conservation issues, but what impact does a zoo visit have on their beliefs or behaviours? Research suggests that visitors are more knowledgeable and hold more favourable attitudes following a zoo visit, but uncertainty remains surrounding the factors that influence this effect.
To better understand how visiting zoos could potentially change visitors’ beliefs or behaviours towards conservation, I interviewed visitors at Chester Zoo to elicit their beliefs. Also, I described strategies being used in activities that communicate education about conservation to zoo visitors. Using the Theoretical Domains Framework, I characterised zoo visitors’ responses into five “important” domains. The evidence gained was used to inform the design of a questionnaire which I implemented in subsequent studies in my PhD.
Current evaluation of the impacts of chemicals and their mixtures on freshwater ecosystems relies heavily on single- and multi-chemical effects on individual species. However, species do not exist in isolation, and a mechanistic understanding of how chemicals and their mixtures impact species interactions is essential if we are to extrapolate from single species, single chemical studies to assessing the impact of multiple chemicals on multispecies assemblages in ecosystems. Here we demonstrate the use of a consumer-resource system to begin to disentangle the complex effects of chemical mixtures on ecological communities. We present the results from a series of crossed-design binary-chemical consumer (grazer)-resource (primary producer) interaction experiments using the freshwater snail, Potamopyrgus antipodarum and the freshwater diatom, Nitzschia palea.
We investigate the Euclidean algebra e(3) = sl2 ⋉ V3 in prime characteristic p > 2. While Bavula and Lu provided a comprehensive analysis of the characteristic zero case, this work develops the theory in the prime characteristic.
The study focuses on the universal enveloping algebra U(e(3)) of the Lie algebra e(3). The goal is to classify simple modules and prime ideals of the algebra U(e(3)). Our main results describe the tensor product structure and the centre of the algebra through precise algebraic relationships. These findings extend the understanding of Lie algebras in a prime characteristic, contributing to both pure mathematics and theoretical physics, particularly in areas where discrete mathematical structures are essential.
Plants release exudates, manipulating the soil surrounding their roots and creating a region called the rhizosphere. Microbiota inhabiting the rhizosphere are adapted to utilise these exudates, composed of simple (e.g., organic acids) and complex (e.g., polysaccharides) carbon sources. Whilst there have been advances in understanding the plant rhizosphere microbiome, the role of polysaccharides in driving microbiome assemblage remains limited. Bacteroidota, an abundant soil bacterial phylum, are typically enriched in plant microbiomes. In the human gut, they degrade dietary polysaccharides, but their role in soil has received less attention. These bacteria possess Polysaccharide Utilisation Loci (PULs), encoding proteins for complex carbohydrate metabolism. However, the mechanisms enabling Bacteroidota to degrade polysaccharides in soil remain unclear. My work identifies specific PULs linked to plant polysaccharide utilisation and their impact on microbiome assemblage.
Aurorae (e.g. the Northern Lights) are not unique to Earth. We see these 'light shows' on almost all of our planets, and beyond our Solar System on objects known as brown dwarfs: too massive to be exoplanets but too cool to be stars. In 2015, LSR J1835+3259 was the first brown dwarf to have confirmed aurora with its simultaneous optical and radio variations. NASA's James Webb Space Telescope has since allowed us to observe at IR wavelengths in unprecedented detail. IR studies of LSR J1835 have revealed 1) it is likely older than suspected, 2) the variability in flux has decreased since previous aurorae observations, and 3) the previous model of variability doesn't work. I therefore present a new model for the variability. I find that between light scattering off radiation belts, dust from an exoplanet companion, and heating/disequilibrium chemistry due the auroral processes, the latter is most likely to physically explain this new model.
As one of the highest emission-intensive foods, chocolate presents a significant challenge in meeting consumer demand and sustainability goals. Focusing on carbon sequestration and climate resilience, this field trial aims to explore the potential of agroforestry and enhanced rock weathering (ERW) as a dual strategy towards net zero cocoa. We here describe how agroforestry systems, particularly multistrata systems such as Cabrucas, can enhance carbon sequestration and delve into the mechanisms by which ERW can augment these benefits, focusing on its impact on carbon accrual, nutrient release, and soil health. This research underscores the importance of integrated approaches to address the complex challenges facing the cocoa sector. Further research is needed to quantify the economic and social benefits of agroforestry and ERW, as well as to develop best management practices for different agro-ecological contexts.
Interstrand cross links (ICLs) are covalent linkages between the two polynucleotide strands of the DNA double helix structure, they are highly toxic due to their ability to impede DNA transcription and replication. Fanconi anaemia (FA) patients are deficient in ICL repair and are therefore cancer-prone. FA arises from mutations in FANC genes, disrupting the FA pathway which repairs ICLs via DNA excision. Recent work has highlighted a secondary, excision-free, ICL repair pathway that remains undefined.
4-Hydroxynonenal (4-HNE), a lipid peroxidation product, forms both native (imine, carbinolamine and pyramidopurinone forms in equilibrium) and reduced ICLs. This work aims to synthesize DNA duplexes containing 4-HNE-derived ICLs to study their structure and repair, potentially involving the non-FA pathway. Progress includes the synthesis of several key compounds, including O6 protected 2-fluoro-2’-deoxyinosine for use in DNA synthesis as well as a 4-HNE derived aminodiol linker compound.
Tissue stiffness is a main regulator during development regulating cell behaviour such as cell proliferation or cell migration. It also plays a major role in diseases such as cancer and fibrosis. However, the underpinning mechanisms are incompletely understood.
My project- if successful- will determine the impact of stiffness on the cell surface proteome, which might help to identify stiffness regulated pathways. Furthermore, insights into the underpinning mechanism might help to develop novel anti-cancer or anti-fibrosis strategies.
Freshwater ecosystems are under threat from multiple environmental stressors yet play a disproportionate role in global biodiversity, containing 10% of described species despite covering 1% of the planet. Ecological models of species interactions are a powerful tool for predicting these stressors' effects by providing an interface between traits and community dynamics. Although considerable trait data exists to inform such models, difficulties with accessibility and species bias often leads to species at lower trophic levels being assigned to larger groups. This aggregation may impact the capacity for models to predict community responses to climate change including diversity, stability and robustness to extinction. To address this, I have produced a trait database for phytoplankton and zooplankton providing information on body size, phylogeny and functional group membership for over 3500 species across 41 countries.
Drug discovery research is heavily reliant on library synthesis to uncover new small molecule ‘hits’ that can be further developed into lead compounds. The availability of multifunctional small molecule scaffolds underpins this activity, as these offer a platform for the generation of libraries of distinct compound sets for downstream biological assays. Moreover, it is essential that such scaffolds have relatively low molecular weight profiles so that they can be elaborated without going over the limits set by Lipinski’s guidelines. In this context, this project entails the synthesis of pyrazolylmethyl trifluoroborate salts, potential precursors of N-benzyl pyrazole derivatives – a privileged class of bioactive small molecules in medicinal chemistry.
Commercial selective logging in tropical forests leads to canopy layer disturbance and the subsequent rapid growth of ruderal, photophilic lianas. Lianas negatively impact tree performance but can benefit fauna by providing fruits, nectar, nests and connectivity. Complete climber removal is used for tropical forest restoration, but a key question is understanding how different intensities of liana removal impact forest regeneration. Using a 320-ha liana removal experiment in Sabah, Malaysian Borneo, we explored the impact of a spectrum of liana removal intensities on liana regrowth, tree growth and carbon storage. We find that the effect of liana removal intensity on overall adult tree growth is positive, but that there was no impact of liana removal at any intensity on overall juvenile tree growth, tree or plot biomass, or carbon stocking. The results also revealed that responses to liana cutting is taxonomy-dependent, and that this could be due to differences in functional traits.
We explored the possibility that dark energy and dark matter could emerge from two fields called dilaton and axion fields. These fields represent the size of extra dimensions and the energy flux wrapping around these compacted dimensions, respectively. We examined how these fields, acting as dark matter and dark energy, influence the evolution of the Universe. In particular, we studied their impact on the formation of galaxies, the development of cosmic structures, and the evolution of the cosmic microwave background (CMB) radiation, which is the radiation left over from the earliest events in the history of the Universe.
Regenerative farming practices have been heralded as an environmentally friendly alternative to conventional, intensive farming practices. The use of leys within crop rotations can improve soil health and promote the biodiversity of microfauna within the soil. A healthy and diverse soil microbial community can promote the health of crops grown in the soils following the leys. However, it has been reported that the crops subsequently grown after a ley suffer a growth penalty. We hypothesise that chemicals secreted by roots of the ley crops are responsible for recruiting and maintaining a healthy soil microbiome whilst negatively impacting the growth of subsequent crops. This project seeks to untangle these probiotic and growth-suppressive chemicals which can increase our understanding of how plants shape the soil microbial community.
Coaxial cables can be used to create networks representing molecules and lattice structures, such as benzene and graphene. In these networks the junctions between cables act as atoms, and the cables as bonds. The resonance frequencies of the network then correspond to the energies of the states in the actual structure. This gives a simple and easy platform with which to study condensed matter systems and look at their properties when disorder is introduced in a controlled way. The main system of interest here will be one dimensional quasicrystal structures, which display an array of interesting properties, such as super band gaps and unusual localisation properties. These quasicrystals are designed using a simple set of rules, connected to Fibonacci sequences. We discuss using coaxial networks to investigate the properties of quasi-periodic systems, contrasting them with periodic and random structures.
Cells are often required to move together as groups to help organisms develop properly and to heal wounds. How groups of identical cells migrate has been studied extensively, but this migration can also be made up of different types of cells. This mixed-cell movement is important for early development and plays a role in cancer metastasis and the formation of secondary tumours. However, how different cell types can co-ordinate their movement remains poorly understood.
To study this, I am using fruit fly embryos, where we recently discovered four different cell types that migrate together in the developing gut. This makes it a great model for studying how different cells can work together to move in a co-ordinated manner. My goal is to uncover the mechanisms that enable collective migration in mixed-cell populations.
Streptonigrone is a natural product derived from Streptomyces, belonging to the same class of compounds as streptonigrin, which has been definitively established as an axially chiral molecule. However, naturally isolated streptonigrone does not exhibit circular dichroism, raising uncertainty as to whether it is an achiral compound or a racemic mixture. Given the crucial role of chirality—particularly atropisomerism—in modern drug discovery, where different stereoisomers often exhibit significantly distinct pharmacological properties such as efficacy and toxicity, determining streptonigrone’s chiral nature is important. However, the synthesis of single atropisomers remains a considerable challenge. To address these challenges, this study aims to develop an efficient and stereocontrolled route to streptonigrone using dynamic resolution of boronic esters. This poster will provide an update on our progress towards the synthesis of this natural product.
Enterococcus cecorum is an emerging poultry pathogen that infects the free thoracic vertebra of chickens, racing pigeons, and pekin ducks causing osteomyelitis, spondylitis, and femoral head necrosis. Rare cases have also been observed in humans where contaminated meat and domestic animals are thought to act as carriers. The spread of the bacteria has been aided by high levels of antimicrobial resistance as well as the emergence of divergent clonal lines which has allowed the organism to improve its pathogenic potential within poultry. To investigate the traits which may be contributing to the spread of these bacteria we investigated both the genomic and phenotypic characteristics of 190 E. cecorum isolates to identify key differences between clinical and non-clinical strains. We identified clinical isolates were phylogenetically distant from non-clinical strains as well as containing high levels of antibiotics resistance and altered cell envelope composition.
Some bacteria self-organise into turbulent flows via self-motility and cell-to-cell collisions, known as active turbulence. A key challenge to our understanding of active turbulence is mapping experimental data to mathematical models. Physics-inspired approaches to modelling typically start from known first principles to construct minimal models. In biology, diversity and complexity is the rule, not the exception, so modellers need to account for how different factors we observe, such as the shape and speed of cells, can be reflected in models to improve the fit to data. New machine learning methods have opened up the possibility of an alternative approach to model building, by selecting the best fitting model algorithmically, while using human-inputted constraints to improve model discovery. We apply a machine learning-based method for learning equations to experimental data of active turbulence in wild and mutant Pseudomonas aeruginosa, comparing the learned models for both strains.
Pancreatic cancers are one of the most aggressive forms of cancer because they manage to survive and grow in nutrient-deprived environments. We hypothesised that Pancreatic Ductal Adenocarcinoma (PDAC) cells could remodel their Extracellular Matrix (ECM) to produce nutrients under nutrient-limiting conditions. Using PDAC cell lines, our preliminary data showed that Matrigel, a component of the ECM supports the proliferation of PDAC cells in Glucose and Glutamine deprivation conditions, as well as in Tissue Interstitial Fluid Media (TIFM), which has been reported to mimic the physiological nutrient availability in PDAC tumours. Importantly, our data showed that the presence of Matrigel can alter the metabolism of PDAC cells and that arginine metabolism is upregulated when the cells are grown under starvation on Matrigel. Overall, our study has established that the ECM can alter the metabolism of PDAC cells to support their cell growth under nutrient-limiting conditions.
We have recently developed a new class of thermoresponsive amphiphilic diblock copolymers that can reversibly switch between up to four copolymer morphologies in aqueous media. A new exemplar of this unique self-assembly behaviour is poly(N,N’-dimethyl acrylamide)-poly(4-hydroxybutyl acrylate) (PDMAC-PHBA).Thermal transitions are sensitive to the precise copolymer composition but typically spheres are formed below 5°C, worms are obtained at around 12.5-17.5°C, vesicles are produced at 25°C and lamellae are formed above 30°C for PDMAC43-PHBA180
This project is focused on two key parts. Firstly, the rigorous analysis using Small Angle X-Ray Scattering of the various shapes that can be specifically targeted to build up a large data set which may be used to develop machine-learning algorithms to assist users. Secondly, the analysis of these polymers using Small Angle Neutron Scattering to determine the exact mechanism of the thermoresponsive behaviour.
Trace metals, such as copper, are essential for life but can become toxic in excess. Traditionally, ecotoxicology has focused on the dose-response of individual metals, often lacking mechanistic insights and overlooking mediating factors like nutrient availability. Using Drosophila melanogaster, a powerful genetic model, I investigate how essential metals interact with nutrients to alter toxicity thresholds. Preliminary findings suggest that dietary composition can impact an organism's ability to cope with copper toxicity during development. Additionally, manipulating a key metal-regulating transcription factor alters the response to copper toxicity under different protein diets, suggesting nutritional dependencies in metal regulation. By incorporating functional genetics into ecotoxicology, we can better understand how organisms handle metal exposure, predict species sensitivity to complex scenarios, and link molecular mechanisms to environmental impacts.
Plants in many regions of the world are experiencing greater drought. They are also experiencing greater nitrogen supply through fertilization and eCO2. Understanding how nitrogen and CO2 control plant responses to drought is therefore critical. Elevated CO2 can increase plant tolerance to drought by closing stomata and increasing water use efficiency. High nitrogen supply may, in contrast, reduce plant tolerance to drought by increasing transpiration. However,the relative importance of CO2 and nitrogen supply in controlling plant drought responses is not known. Little is known about how nitrogen and CO2 interact in combination, to control plant drought responses.This project will use a variety of plant physiology approaches to determine the importance of nitrogen and CO2 in plant drought responses. It will include assessments of photosynthesis, transpiration, stomatal conductance, and WUE in plants exposed to either increased nitrogen supply, eCO2, or both in combination.
Development of a medium to high throughput light-sheet fluorescent microscope including two wavelengths, 488nm(green) and 561nm (red). This lightsheet will be used in tandem with a zebrafish sorting robot that will collect individual fish from a 96 well plate and place them into the FOV of the light-sheet system, allowing for precision positioning of the zebrafish with high repeatability, and higher throughput of individual zebrafish samples. The lightsheet will be formed using 2 galvanometer scanning mirrors which are rapidly scanned along the Y plane, and the creation of a 3 dimensional image is done using a slower scan in the Z plane. An electrically tunable lens will be used to account for the focal point changes as the laser is scanned through the zebrafish sample. Once the two systems have been joined, I will use the system for drug screenings, specifically for Schwann cell recovery in the PNS due to mutations in the Adgrg6 protein.
Communication begins early in infancy, long before the emergence of words. During this period, infants engage in prelinguistic behaviours—such as gestures, gaze, and vocalisations—that lay the groundwork for later language development. However, early deafness can disrupt prelinguistic communication and this may put children at risk of language delays (Lederberg et al., 2013). Kelly et al. (2020) found that deaf infants of hearing parents (DOH) produced fewer prelinguistic behaviours than hearing infants of hearing parents (HOH) during parent-infant interactions. However the study sample size was small and the wider literature reports mixed findings. This study aims to conceptually replicate Kelly et al. (2020) and extend it by including children with mild hearing loss. This will illuminate the role of experience in the development of communication and language and tell us whether therapeutic support is needed in the first year (potentially before cochlear implant).
Urbanization is rapidly accelerating, and globally most humans now live in urban areas. Indonesia, for example, has the second highest urbanization rate in Asia, with it increasing from 33% to 51% in twenty years (1992-2012), with most of this concentrated in Java. Urbanization's effects depend on the rate and magnitude of environmental change, but generally urban development causes a decline in biodiversity. Although urbanization is already established as a major driver of biodiversity loss and biotic homogenization, empirical studies from tropical locations, especially ones focusing on invertebrates are limited. This research will tackle this gap. It will address questions regarding how butterfly communities respond to urbanisation in Java, Indonesia, focusing on changes in biodiversity (species richness and abundance), the species traits associated with tolerance to urbanisation, and how butterfly genetics, colour and morphology are influenced by urbanization.
My project is focused on studying how the stringent response affects ribosomal maturation and regeneration in Staphylococcus aureus. The stringent response is a stress signal that bacterial cells activate when they are stressed, for example, due to low nutrients in their environment. The activation of this response results in a down-regulation of a variety of essential pathways in cells such as translation and transcription, with the end goal of reducing the energy expenditure of the cell allowing it to enter a hibernation state. This results in cells not being able to continue dividing. The effects of also affect the process of ribosomal biogenesis/maturation. Ribosomes are complex machineries that are responsible for the production of proteins in cells, understanding the maturation process of these particles could allow for broad-spectrum antibiotic discovery.
Quantum technologies promise to deliver numerous benefits and revolutionise the way we process and share information. Whilst the theoretical background is well understood, it remains challenging to realise quantum information processing systems in reality. This is primarily due to the issue of dephasing, whereby a quantum state loses its coherence through interactions with its macroscopic environment. This work focuses on the interactions between quantum dots - a promising platform for quantum information processing - and their environment, including spectral diffusion and phonon coupling.
Shelf seas are among the most productive ecosystems on Earth, playing a crucial role in nutrient cycling, climate regulation, and food production. Benthic macroinvertebrates are key components of these ecosystems, forming a highly diverse component of marine food webs. Despite the ecosystem services they provide, the high sensitivity of benthic invertebrates to external stressors is causing shifts across benthic habitats globally. While benthic communities are not routinely monitored at large spatial scales, many smaller surveys have now been aggregated into openly available biodiversity databases. These datasets can be combined with species traits data and phylogenetic information to quantify benthic community variation across time and space, highlighting trends across multiple dimensions of diversity. The spatial mapping of each dimension can provide valuable insights for marine conservation, enabling the prioritization of management strategies throughout the European marine benthos.
Self-assembled nanostructures of β (beta) and α (alpha) stereoisomer amino acids have garnered significant attention in drug delivery and other applications due to their unique properties. These amino acids, the fundamental building blocks of proteins, are capable of self-organizing into nanostructures at the molecular level. The distinct structural and functional characteristics of the β and α forms influence their interactions within biological systems. When applied to drug delivery, these nanostructures can improve the stability, targeting, and controlled release of therapeutic agents. Moreover, their biocompatibility and versatility make them well-suited for a wide range of applications, including tissue engineering, biosensing, and regenerative medicine, thus presenting promising avenues for advanced medical treatments.
Phosphoinositides are phospholipids that provide identity to membrane-bound compartments. In phagocytosis, they temporally coordinate effector molecule delivery to the maturing phagosome. PIKfyve, a phosphoinositide 5-kinase, functions in a complex with the phosphatase Fig4 and the scaffold protein Vac14 to convert PI(3)P to PI(3,5)P2.
Activation and regulation of the PIKfyve complex remain poorly understood. Loss of PIKfyve causes swollen endosomes and delayed bacterial killing due to impaired V-ATPase and hydrolase delivery. In mammalian cells, loss of Vac14 or Fig4 causes neurodegeneration, but their roles in phagocytosis are less explored.
I made Vac14 and Fig4 CRISPR knockouts in Dictyostelium discoideum, a slime-mould amoeba and professional phagocyte. Fig4- cells show minimal phenotypic differences from WT, while Vac14- cells exhibit reduced proteolytic activity. Notably, PIKfyve localises to the phagosome membrane in Vac14- cells but fails to convert PI(3)P to PI(3,5)P2.