Constitutive secretion is essential for delivering newly synthesized proteins to the cell surface and extracellular space, enabling the transport of key molecules like antibodies, cytokines, and extracellular matrix components. Disruptions in this pathway are linked to diseases such as cancer, neurodegeneration, and inflammation. Membrane fusion, driven by SNARE proteins, is crucial for protein secretion, but the specific SNARE complexes involved remain unclear. The Peden lab developed a genetic assay using Botulinum toxin (BoNT/X) and cleavage-resistant SNARE proteins, identifying Ykt6 as the only SNARE protein capable of fully rescuing BoNT/X-induced disruption. My research investigates the structural components necessary for Ykt6’s function, using genetic mutations in cleavage-resistant Ykt6 to test its ability to rescue BoNT/X intoxication. Preliminary findings suggest lipid modification may be more crucial than intracellular localization for Ykt6’s function.
Staphylococcus aureus regulates virulence and biofilm formation through the agr-mediated quorum sensing (QS) system, making it an attractive target for anti-virulence therapies. In this study, we design and evaluate β-amino acid-containing peptides as potential QS inhibitors. The QS inhibition efficacy is assessed in vitro using a bioluminescence reporter system, where fluorescence intensity serves as an indicator of QS activity. Our results demonstrate that β-amino acid peptides exhibit remarkable enzymatic stability, significantly enhancing their in vivo half-life. Furthermore, even when β-amino acid residues are incorporated into an α-amino acid peptide backbone, they provide substantial protection to adjacent peptide bonds against enzymatic degradation. This work highlights the potential of β-amino acid-modified peptides as stable and effective QS inhibitors for combating antibiotic-resistant S. aureus infections.
Urban ecosystems (UE) are complex spaces where humans, fauna, flora and environmental factors interact. Urban forests, a significant component of UE, provide key ecosystem services (ES) and support a complex network of interdependent biota. However, they are often impacted by several abiotic stressors including the urban heat island effect (UHI), tropospheric pollutants and drought. Understanding the broader negative ecological consequences of stressor-induced trait changes at an ecosystem scale is important, as how these organisms cope with multifaceted stressors remains poorly understood, and often-overlooked. This research aims to address how urban forests, termed “treescapes”, respond to a complex mixture of abiotic stressors, and in-turn, how this modulates tree-insect interactions. The project employs a multidisciplinary approach disentangle the complex interactions between trees, their environment, and dependent biota.
Wide bandgap perovskite photovoltaics are promising for indoor energy harvesting, particularly in low-power electronics and Internet of Things (IoT) applications. However, phase segregation remains a major challenge, affecting efficiency and stability. In this study, we focused on characterizing phase segregation in Cs₀.₂FA₀.₈Pb(I₀.₄₅Br₀.₅₅)₃ perovskite films using advanced spectroscopic and imaging techniques. These methods provided a detailed analysis of ion distribution before and after light illumination, revealing crucial insights into the dynamic evolution of halide segregation.
The mechanisms underlying the functional development of the auditory pathway are still largely unknown. In analogy with other sensory systems, it has been hypothesised that spontaneous neural activity present in the early developmental stages affects the formation of the auditory pathway.
However, how immature auditory circuits are assembled and how they are affected by dysfunction of the sensory cells is still poorly understood.
Addressing this unknown is currently impractical in mammals due to the complexity of the nervous system and inaccessibility of the inner ear. Therefore this project aims to use the zebrafish, a small vertebrate with a sophisticated sense of hearing.
Crucially, the small size and transparency of the fish will allow us to use fluorescence imaging to monitor how auditory stimuli are encoded by the ear and the brain in-vivo. When combined with targeted disruption of peripheral activity, this project will unravel the mechanisms behind the maturation of the pathway.
Paranoia involves mistrust, suspiciousness, and beliefs of persecution, existing on a spectrum with ordinary mistrust. While extreme paranoia is often classified as delusional, its distinction from other strong beliefs, such as conspiracy theories or religious beliefs, remains unclear. This research examines the common psychological factors underlying these beliefs, focusing on two key areas: intolerance of uncertainty (IoU), testimonial competence. IoU may contribute to both paranoia and strong beliefs by influencing how individuals cope with ambiguity. Additionally, paranoia differs from other beliefs in its isolation, as paranoid individuals often struggle to share or validate their beliefs with others. This may be due to impaired testimonial competence, which affects their ability to engage in belief-sharing, which hinder their understanding of others' perspectives. Together, these cognitive factors may play a crucial role in the development and persistence of paranoia.
Butterflies display diverse colours that serve functions including signalling and thermoregulation. Butterflies regulate wing temperature through mechanisms such as differential absorption of visible, ultraviolet, and infrared wavelengths. Large-scale studies on colour trends across environments are understudied, and the correlation between reflectivity in different spectra remains unclear. This study examined butterfly wing reflectivity in various spectra and environments. We found that environment and phylogeny, rather than close relatedness, shaped colouration. Butterflies in warmer environments had higher reflectance across all spectra, suggesting limited reflectivity in cooler environments due to niche selection. Size affected brightness most in the ultraviolet spectrum, where smaller wings were more UV reflective, indicating a trade-off between size and UV reflectivity.
We consider the random trees commonly known as Galton-Watson trees; a 'branching process' where each individual has a random number of children, based on some random distribution (if the average number of children is less than / equal to / greater than 1, we call the tree sub-critical / critical / super-critical). Sub-critical and critical trees are finite with probability 1, while super-critical trees may be infinite. We "condition" (force) the sub-critical and critical trees to be large in some way (height, number of nodes, etc) and attain a certain result in what we call their local limit. This limiting tree was first discovered by Harry Kesten in 1986, who found that when conditioning a sub-critical or critical tree to have height n, in the limit of n, we attain a tree with only one infinite line of descent. Our research considers other ways to attain the same limiting tree, which we call the Kesten tree, including conditioning based on “types” which are assigned to each node.
To survive changing conditions and adapt to their environment, bacteria maintain a complex cell wall that is continually restructured. One understudied family of enzymes that plays an important role in this adaptive restructuring process are the LD-Transpeptides (LDTs). These LDTs catalyse a number of reactions that reshape peptidoglycan (a major component of the bacterial cell wall) and increase its resistance to stress. Bacteria like Rhizobium leguminosarum, which form an agriculturally important, nitrogen-fixing symbiosis with plants, contain many of these LDT enzymes — often 17 or more. Whilst all of these enzymes belong to the same family, data reveals that some of these enzymes are more important than others when it comes to forming a successful symbiosis. Here we take a closer look at the individual LDT enzymes from R. leguminosarm and attempt to determine their individual contributions to peptidoglycan remodelling and symbiotic fitness.
The aim of this study is to functionally characterize Rex3, a putative exonuclease, by identifying its RNA substrates and determining its role in RNA processing. Additionally, I will investigate the structural features required for Rex3's function in vivo. While sequence homology suggests that Rex3 is involved in RNA metabolism, its exonuclease activity has not yet been experimentally confirmed. Therefore, this project will focus on characterizing Rex3's enzymatic activity and understanding its biological significance in RNA processing pathways.
Aqueous polyurethanes (PU) offer a low-volatile organic compound route to environmentally friendly, high-performance coatings. For effective product development, it is necessary to understand and control the morphologies of the dispersions. This study investigates how variations in hard block content and thermomechanical processing influence the final paint performance. By employing small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM), we aim to analyse the particle structures both in dispersion and in films, establishing key correlations to enhance formulation strategies.
Black holes have diverging spacetime curvature forming a singularity. A positive-mass black hole has a horizon, beyond which nothing can escape. Negative-mass black holes are forbidden, as they do not have horizons around their singularity.
General relativity can’t be consistently applied on small scales. To accurately describe the physics near the singularity of a black hole we need an extension called quantum gravity.
If quantum effects resolve the singularity, negative mass black holes could exist, destabilizing the vacuum and requiring an explanation for their absence.
Changes of space and can be described by a metric. We also include a cosmological constant Λ in our description together with the unimodular time T.
We quantise the metric and impose unitarity with respect to unimodular time T.
A quantum theory constructed this way includes either only positive, negative or zero mass black hole states. Also we find that the black hole singularity is resolved.
Threat beliefs encompass persecutory delusions observed in clinical populations, as well as beliefs held by the general population, such as persecutory supernatural beings. Prior research has predominantly focused on the neural and cognitive mechanisms underlying persecutory delusions, yet their overlap with other forms of threat beliefs and the role of the social environment in shaping these experiences remains underexplored. This study aims to: i) examine the phenomenological similarities and differences between perceived threats from supernatural beings (e.g., demons) and human beings, and ii) explore the extent to which the socio-cultural context mediates meaning-making and attributions of persecutory intent. Fieldwork and qualitative interviews (n=20) are being conducted with participants from an Evangelical church who report experiences of demonic attack, and individuals from peer support groups for paranoia, utilising Interpretative Phenomenological Analysis to analyse data.
Insects are declining due to numerous anthropogenic factors, including urbanisation. Although urban greenspaces and interventions such as wildflower areas can be important pollinator habitat, the effects of urbanisation on the quality of floral resources remain poorly understood. Abiotic environmental stressors, e.g., pollution, drought and heat stress, can disrupt plant-pollinator communication, and affect pollen and nectar quality, although no studies have directly tested how the changes in reward quality impact pollinator health. Understanding how abiotic stressors impact pollinators and floral resources is key to urban pollinator conservation. We established a long-term field experiment, controlling habitat quality and floral resource availability across different levels of urban stress, to ask: how do pollution intensity and other urban stressors impact 1) the abundance and diversity of pollinating insects and 2) the quality of floral resources for pollinators?
Artificial photosynthesis (AP) is at the forefront of solar chemistry research. Pt(II) donor-bridge-acceptor complexes hold potential as AP systems due to their extensive electron transfer pathways upon irradiation with light. The nature and lifetime of the excited states formed can be modified through variation of both the strength of the donor/acceptor moieties and also the extent of electronic coupling to the Pt(II) bridge. A particular state of interest is the charge separated state (CSS) due to its high potential energy. The aim of this project is to design and synthesise complexes that could exhibit the CSS, investigate their electron transfer pathways using ultrafast spectroscopic techniques, and externally control the lifetime of the desirable states. Control is applied via specific infrared laser perturbation which, when applied to specific vibrations within the molecule, can selectively increase or decrease the yield of a certain electron transfer pathway.
Enhancers are cis-regulatory elements that boost transcription of their associated genes. Histone acetylation by CREB-binding protein (CBP) bound at enhancers relaxes chromatin structure and increases enhancer accessibility to other transcription factors. When activated, enhancers are transcribed into non-coding enhancer RNAs (eRNA). RNA binding can activate CBP, enhancing its ability to modify histones and promote transcription, highlighting the dynamic interplay between eRNA, enhancers, and CBP in gene regulation⁴. However, the role that RNA structure plays in this regulation has not been fully investigated.
For decades fluorescent proteins (FPs) have played an essential role in both biological and medical research. As FPs are genetically-encodable fluorescent markers they can be used with macroscopic imaging methods to observe different cell structures at the level of individual molecules. However, FPs have their limitations with both photobleaching and phototoxicity causing problems in fluorescence microscopy. Little is known about the mechanisms of these processes but it is theorised that the triplet state plays an important role in these mechanisms. Recently it has been shown that reverse intersystem crossing (RISC)might play an important role in reducing photobleaching, and that this RISC pathway can be used to make a fluorescent protein spin qubit. Using transient absorption in the NIR region we hope to better understand triplets in various FPs, with the hope of figuring out how we can improve FPs to make them more robust and encourage further development.
Metalated tetrapyrroles are macrocycles that contain a central metal ion inserted by a chelatase enzyme. These molecules play essential roles in important processes, such as photosynthesis and respiration. Examples include (siro)hemes (containing Fe inserted by a ferrochelatase, FeCH), and chlorophylls (Mg, magnesium chelatase, MgCH). Biosynthesis of the modified tetrapyrroles is via a central pathway that deviates at key points. The chelatase enzymes act at these branches, making their regulation important for balancing the respective end products. For example, phototrophic bacteria such as Rhodobacter sphaeroides can switch between aerobic respiration in oxygenic conditions and photosynthetic growth in anoxic conditions, making the regulation of MgCH and FeCH crucial for balancing flux between the heme and bacteriochlorophyll biosynthesis pathways. This work aims to understand chelatase enzymes and their mechanisms of action and regulation, primarily adopting a structural approach.
The detection and analysis of trace gases are crucial in environmental and industrial monitoring, particularly for mitigating the impact of global warming and ensuring air quality. This thesis explores advanced photoacoustic spectroscopy (PAS) techniques for the detection of key atmospheric gases, including carbon dioxide (CO₂) and hydrogen sulfide (H₂S). Focusing on Near-Infrared (NIR) applications, this work evaluates the performance of different PAS systems, such as Resonant Photoacoustic Spectroscopy (RPAS), Quartz-Enhanced Photoacoustic Spectroscopy (QEPAS), and Cavity Enhanced Resonant Photoacoustic Spectroscopy (CERPAS). The study also incorporates Distributed Feedback (DFB) lasers to improve detection sensitivity and specificity. The experimental analysis includes a comparative assessment of these PAS techniques and investigates their detection limits and sensitivity when applied to trace gases in both air and natural gas environments.
Species have evolved life history strategies optimising survival, reproduction, and growth during different life stages. However, this presents an evolutionary puzzle regarding early development. Juvenile mortality is often higher than later life stages, so selection from time-dependent mortality during early stages should favour faster strategies. However, developmental durations vary extensively.
Birds have played a key role in identifying drivers of this variation. Research highlights the importance of intrinsic traits such as body size, physiology and trade offs with later stages. Similarly, ecological traits like diet and migration are also associated.
However, broad scale analyses also report high phylogenetic influence, and ecological conclusions may be confounded with ecomorphology. Shorebirds present an opportunity to limit these considerations. We use modern comparative methods to test traits for associations with this key life history variable within a diverse group.
Van der Waals materials are an exciting class of semiconductors composed of atomically thin layers held together by weak interlayer forces. By carefully tuning their interactions with light, we can reach the strong coupling regime, where light and matter merge to form hybrid quasiparticles known as polaritons. This phenomenon unlocks new possibilities for future technologies, from energy-efficient lasers to quantum computing. In this research, we demonstrate how strong coupling can be achieved at room temperature and actively controlled by leveraging the optical properties of ZrSe3, paving the way for potential compact, and tuneable photonic applications.
Hearing loss is the most common sensory deficit in older adults, with the vast majority being age-related or progressive hearing loss. One of the most common causes is genetic mutations that impair the structure and function of the auditory sensory hair cells in the inner ear. These are responsible for translating sound waves into nerve impulses that are relayed to the brain for processing. There has been success in using gene therapy to treat pre-lingual deafness, however it is not known whether the same approach can target more progressive, post-lingual forms of hearing loss. My project investigates pre-clinically if gene replacement therapy via adeno-associated virus (AAV) delays the progression of hearing loss due to mutations in BAIAP2L2, a protein essential for sensory hair cell development and function, and the therapeutic time window for treatment.
Per- and polyfluoroalkyl compounds (PFAS) are substances that are widely used in textiles, surfactants, food packaging, non-stick coatings and firefighting foams etc. due to their many advantages such as durability and stability. However, PFAS can enter the human body through inhalation, skin contact, ingestion of food and drinking water where they can potentially lead to cancer, immune system suppression and hormonal disruption.1,2
Adsorption is a common method for removing perfluorinated and polyfluorinated alkyl compounds (PFAS) from wastewater. In this study, hypercrosslinked polymers with good adsorption uptakes are investigated. A batch of hypercrosslinked polymers (HCPs) with high surface areas were synthesised using 1,4-bis(chloromethyl)-benzene and 4,4'-bis(chloromethyl)-1,1'-biphenyl, polystyrene, etc.
The results of the adsorbents for PFOA adsorption will be discussed, and the adsorption process of PFOA by these HCPs will be described using isothermal adsorption modelling.
Convergent evolution occurs when organisms independently evolve similar traits. Studying Convergent evolution offers a fascinating lens through which to examine how similar environmental pressures, and ecological niches have shaped the evolution of distinct species, and lineages. Studying this process in grasses helps us understand the underlying genetic, and evolutionary traits that enable organisms to adapt to extreme conditions. It provides insights into how different genetic paths can lead to similar adaptive outcomes, highlighting the flexibility and creativity of evolutionary processes.
Exceeding 26% efficiency with improved output power stability in recent years has made researchers more optimistic about the commercialization of perovskite solar cells as a future photovoltaic technology. However, one of the issues hindering their industrialization is the development of non-toxic solvent-based ambient preparation techniques for perovskite thin films, which can reduce manufacturing costs by eliminating the need for an inert gas-filled glove box. In this work, we show that the combination of methylammonium chloride (MACl) with excess lead iodide as an additive to perovskite precursor ink can stabilize the intermediate α-phase of FAPbI3 during coating process in ambient air leading to δ-phase impurity-free uniform perovskite thin films with improved crystallinity. Accordingly, nearly pure FAPbI3 -based perovskite solar cells were developed in high relative humidity air (> 40%) using a triethyl phosphate (TEP)-based green solvent system that delivers a high PCE of 18.6%.
A charge generates an electric field which also affects the charge itself. This is called the self-force (SF) and been studied since the early 1900s as an interesting theoretical problem. More recently, it has also had experimental motivations, since the discovery of black holes with stars/smaller black holes in orbits around the central black hole. These objects feel a gravitational SF, and this drives them towards the eventual merger. Since the experimental detection of gravitational waves, we have been able to detect and model the orbits of many such two body systems or binaries using SF theory and other approaches to the two-body problem. In this work, we study the SF for a fixed charge outside a constant density star, the Schwarzschild star. We find that as the charge approaches the surface of the star, the SF diverges. We present numerical and analytical approximations for the force in this region and closed form results and numerical data away from the surface.
Selfish genes prioritise their own survival at the expense of that of the whole organism. One such selfish genetic element is an X-linked meiotic driver found on the X chromosome of the stalk-eyed fly species Teleopsis dalmanni. This selfish gene targets and blocks development of sperm carrying Y chromosomes. Male T. dalmanni that carry it can only produce X-bearing sperm, resulting in massively female biased sex ratios. Despite its significant ecological impact, the mechanisms, origins and genetic consequences of the T. dalmanni meiotic driver are unknown. Here, using DNA data from a number of T. dalmanni individuals, I aim to understand the population level genetic impacts of the X chromosome drive system, how it evolved, and what genes underlie it. Using DNA data from a number of T. dalmanni individuals I am employing a range of quantitative genetics techniques to look at the structural differences between chromosomes with and without the X-linked meiotic driver.
Description of techniques used in order to fabricate atomically thin structures without the need of using any chemic substances. In addition, a brief explanation of the properties that the fabricated structures showed when excited with white light.
Light is crucial for plants as a source of energy and information. Plants detect light using photoreceptor proteins, with phytochromes being red and far-red(FR) light primary photorecepters.However, evidence suggests chloroplasts, where photosynthesis occurs, may act as environmental sensor, detecting FR. Unpublished data showed that in plants lacking phytochromes, several genes behave similarly to those in plants with phytochromes, responding to the oxidation state changes in photosynthetic components due to FR or herbicide. In short, these genes respond to FR detected by the chloroplast, not phytochromes. Among them are members of the Protein Arginine Methyltransferase(PRMT) family which catalyse methylation at arginine residues. PRMT may be components of a retrograde signalling pathway which is the feedback from chloroplast to nuclease modulating gene expression and responses to the environment. This study aim to investigate the role of PRMTs in light signalling in the model plant.
Heterocyclic boronic acids are essential building blocks for creating complex molecules, with significant applications in medicinal chemistry and material science. Since many small-molecule pharmaceuticals contain saturated heterocycles, having access to saturated heterocyclic boron-based building blocks is highly desirable. However, current commercial availability of these building blocks is limited.
In this project, we developed a method to prepare boronic ester lactams using a conjugate borylation-cyclisation strategy using amino enoates. Initially, we used SIMes as an achiral ligand, producing racemic boronic esters. Later, we employed (S,S)-FOXAP as a chiral ligand, successfully obtaining enantiomerically enriched boronic esters in good to excellent yield. The reactivity of the boronic esters has been explored to demonstrate their potential as chemical building blocks.
This combined theoretical and experimental work investigates the effect of environmental factors on the collective behaviour of quantum dots (QDs) in photon-based systems, essential for scalable quantum technologies. Light emitted from a group of indistinguishable atoms arrives in a short, high-intensity burst known as superradiance. This phenomenon results from many-body entanglement due to indistinguishability of the QDs. While there has been much study of superradiance in free space and structured waveguides (WGs), the potential of chiral coupling in 1D systems has yet to be explored. We aim to observe superradiance in directional WGs and see how dephasing, chiral contrast, and phase separation impact dynamics. Using established theory, we construct a model to explore how environmental factors influence observable superradiance. Simulations show superradiant behaviour is enhanced when QDs are chirally coupled, facilitating our understanding and control of many-body quantum effects.
In algebraic topology, one looks to extract information about topological spaces (which we think of as a generalised version of shapes) via algebraic information associated to these spaces (which we think of as generalising integers). Often, one can use similar techniques to extract information about objects from algebra. A standard algebraic object to study is called an algebra with involution and one such technique to study them is known as the reflexive homology of the algebra. This extracts classical information about how non-commutative the algebra is, along with information about a specified operation that the algebra is equipped with called an involution.
One often wishes to systematically study where theories like reflexive homology really come from, and the answer lies in operads. These are gadgets which slickly encode how many ways there are to multiply together objects. Each operad encodes a certain type of homology, and we determine which one encodes reflexive homology.
The discovery and characterisation of novel enterococcal bacteriophages is necessary to understand the molecular mechanism that underpins enterococcal surface recognition. The Enterococcal Polysaccharide Antigen (EPA) has been described as an essential cell envelope component for phage infection. Little is known about Enterococcal phage receptor binding proteins and how EPA structure contributes to recognition by these viruses.
We isolated 56 phages from different environmental samples that target clinical strains of Enterococci. Using efficiency of plating assays, we successfully characterised the substrate binding specificity of 6 isolated phages against several EPA structural modification OG1RF E. faecalis mutants. This work revealed a high diversity of cell surface recognition strategies by phages and is an important step towards identifying distinct classes of phages that target different surface structures for the design of phage cocktails as therapeutics against these pathogens.
When giant gas clouds collapse under their own gravity, groups of stars form. These groups can be hundreds to thousands of stars, which may be bound together by gravity; this is a stellar cluster. Through interactions between the stars these clusters change shape, spread out, and eventually dissolve into their host galaxy, as stars will get so far away that they are no longer held in by the gravity of the cluster. We use simulations to see how these clusters evolve over time, and what effect the host galaxy has on the evolution and dissolution of stellar clusters.
We find that the force of gravity from the host galaxy always drastically changes the shape of a cluster. However, it can make some clusters dissolve faster, and others slower, than if there wasn’t a host galaxy. This is because, after stars have left the cluster, the gravity of the galaxy can pull some stars back in. In smaller clusters this has a huge effect, but on larger clusters it is mostly negligible.