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  • (2021) Arman, Seyedyousef
    Thesis
    Impedance cellular biosensors are amongst a promising type of label-free technologies in providing ongoing insights into physiological function of cells over a period ranging from several minutes to several days. However, detection of a highly specific biomolecular event using traditional impedance assays is technically challenging. The nature of impedance signal relies on the changes in the local ionic environment at the interface, providing many biochemical events at once lacking biomolecular specificity. The next decade is then likely to witness an interest in using developed impedance assays. Impedance-quartz crystal microbalance (QCM), impedance-surface plasmon resonance spectroscopy (SPR), and impedance-optical microscopy are the hybrid approaches that have been employed in the field. Integrating impedance biosensors to another sensing method, in particular new microscopies that enable identification of cellular structures and processes with a high degree of specificity, enhances the potential of traditional assays by providing additional relevant information. Herein an effective approach for accurate interpretation of impedance signal is presented. By development of optical/electrical multi-electrode chips, light was utilized for direct visualization of cell structures and processes on the surface of the microelectrode. It was essential to achieve both high throughput electrical results and high-resolution microscopy images to detect the transient changes inside the cells. Therefore, the strategy of simultaneous dual sensing was developed in three main steps. For the establishment of a reliable dual sensing readout, it was essential to use a commercial biosensing device (known as xCELLigence) in the first step. This approach enabled to compare the electrical results of developed dual biosensing device and a commercial device (as a high throughput assay for electrical measurement of subtle changes within the cell monolayer). The highly sensitive measurement of commercial device also made it possible to investigate the ongoing mechanism behind receptor/ligand activation. The signalling pathway was determined by using different pharmacological inhibitors. In a separate parallel experiment, fluorescence microscopy was used to visualise the specificity of histamine/HeLa cell interaction which was coupled to intracellular calcium rise. While it is assumed these two processes are connected, this could not be determined definitively by the sole biosensing device application. In the second step it was necessary to develop a setup with the capability of data acquisition in both the high throughput electrical setup and high-resolution fluorescence microscopy on a single platform. The first material of choice for the fabrication of this biosensor was ITO because of its electrical conductivity and optical transparency. It was shown that contribution of cells to the overall signal on the surface of ITO depends on the parameters including sensing area and width of microfingers. Furthermore, comparing the ITO results with the identical gold microelectrode revealed the ITO severely lacked sensitivity compared to gold. This was due to a better penetration of the electric field within the cell layer on the gold surface. The addition of a viewing window made a dual sensing readout possible on the gold microelectrode. Finally, the finding were used to maximize the system efficiency and precision for the detection of minute change of cells to the drug. The reduction of the microfingers down to the single cell level led to a more efficient distribution of electric field within cell monolayer. A high density of gold electrode arrays also increased the chance of individual cells blocking the current which was desirable. The added value of the developed biosensor was illustrated by studying GPCR activation in a more thorough manner using simultaneous fluorescence microscopy. The simultaneous optical/electrical experiment was performed as a powerful approach to translate specific intracellular biomolecular event contributing to the morphological changes in cell/drug interaction.

  • (2021) Moazzam, Parisa
    Thesis
    The expression levels of immune checkpoint inhibitor biomarkers including programmed death-ligand 1 (PD‐L1), cytokine lymphocyte antigen 4 (CTLA-4) and B7-homolog3 (B7-H3) can be used to identify the presence of diseases, and also show a good correlation with therapeutic outcomes. Invasive solid biopsies are used to achieve samples with immunohistochemistry assays being the detection method of choice to identify the expression levels of these biomarkers in clinical practice. These assays are qualitative or semi-quantitative due to biopsy heterogeneity. There is an unmet clinical need for quantitative detection methods that are less invasive, to improve the efficacy of treatments that are closely associated with PD-L1, CTLA-4 and B7-H3 expression levels. The detection of PD-L1, CTLA-4 and B7-H3 in whole blood is an attractive pathway for the early detection, prediction and evaluation of cancer treatment response because of its simplicity but remains almost completely unexplored. The challenge is that a limit of detection of less than picomolar must be achieved for a detection technology to satisfy the requirements of the unmet need. The purpose of this work is firstly to address the unmet need for improved conventional immune checkpoint inhibitor biomarkers detection techniques by designing an ultrasensitive quantitative biosensor based on gold-coated magnetic nanoparticles, referred to as dispersible electrodes. The research demonstrates the ultrasensitive, selective and rapid electrochemical detection of PD-L1, CTLA-4 and B7-H3 directly in whole blood. These dispersible electrodes selectively capture analytes within biofluids and upon application of a magnet, they are reassembled into a macroelectrode for electrochemical detection of the target antigen using a classic sandwich immunoassay with a detection range of nanomolar to attomolar and a response time of only 15 min. The research then focuses on how this system is capable of detecting these species in whole blood without being completely fouled by proteins. Investigations show that ‘soft protein corona’ layer forms around the antibody-modified particles, which can be resulted in lower signal intensity and greater uncertainties of dispersible electrodes but does not completely suppress electrochemistry.

  • (2022) Gautam, Shreedhar
    Thesis
    Extracellular vesicles (EVs) are phospholipid membrane bound sacs (vesicles) produced from almost all types of cells. They are found in circulation and contain the cargo biomolecules such as nucleic acids, proteins, lipids, and amino acids. EVs are involved in trafficking these biomolecules between cells and as such have the role in physiological and pathological processes. EVs are heterogenous and revealing their heterogeneity is crucial to understand their explicit physiological and pathological roles. Current isolation techniques cannot sort EVs based on their biogenesis and provides average information instead of each EVs subtype. Thus, single EVs analysis was popular and many surface protein characterization techniques are developed. But there are no techniques available for internal cargo analysis of individual EVs. The overall aim was to develop a technique to analyse internal microRNA cargo content, if possible, for single EVs, if not from the minimum number of EVs. To achieve that goal, light activated electrochemistry, a technique where focused light beam was illuminated on the semiconductor surface and make it electrochemically active was used. The surface was protected against oxidation during electrochemical reactions by grafting self-assembled monolayer of 1,8-nonadiyne. Then, silicon-based surface was patterned with polymers, antibodies, and cells using the light patterns. As a result, the first milestone to prepare light-assisted patterned semiconductor surface was achieved for our overall aim of analysing content of individual EVs. The size range of EVs is 30 to 200 nm, still very low compared to 30 µm which is the best spatial resolution achieved for light activated electrochemistry using crystalline silicon. Thus, chapter 4 developed a technique to improve the spatial resolution of light activated electrochemistry using amorphous silicon. Amorphous silicon has short diffusion length of charge carriers compared to crystalline silicon due to the defect states in band gap called as localized states. So, charge carriers are frequently trapped in these localized states leading to 60 times improvement in spatial resolution to 500 nm. But even this spatial resolution was not enough to analyse individual EVs. So, microRNA content from pool of EVs were detected using the screen-printed electrodes in a high throughput manner instead of single EVs.

  • (2022) Guo, Haocheng
    Thesis
    To develop faradaic electrodes that integrate advantages of both battery (high capacity), and supercapacitor (fast rate and excellent cycle life) is revolutionary to transform our use of electrical energy, but presents a grand challenge in energy storage. Because their origins are intrinsically conflicting: high capacity requires in-depth redox reactions and longer diffusion distance of ion-charge-carriers, but the corresponding kinetics typically slow down as consequences. Recently, the emerging proton electrochemistry facilitates developments of batteries where proton/hydronium serve as ion-charge-carrier (named as proton batteries) and offers new opportunities for the long pursuit. This thesis aims to understand fundamental working principles of proton electrochemistry, design novel electrode-materials and electrolytes, and correspondingly develop full batteries. Charge storage controlled by diffusion and phase transformation of electrodes are representative indicators of sluggish kinetics in battery chemistries. However, fast rate-capabilities are reached in a α-MoO3 electrode that presents both features associating with protons. In Chapter 2 and 3, this unique topochemistry is disclosed to involve sophisticated ion-electrode-interactions and contains two key steps: hydronium adsorption on surface, and the subsequent naked proton insertion in bulk electrode lattices to trigger irreversible structure transformation to hydrogen molybdenum bronzes (HMBs) from the parent MoO3. Following rearrangements take place only among HMBs phases and present high reversibility and kinetics, therefore structural explanations to the fast rate-capability are provided. At electrode-electrolyte-interfaces, hydronium is determined as the active ion-charge-carrier to initiate charge transfer as well as surface hydration, where water adsorption/expelling with reduced polarizations and enhanced kinetics is accompanied in the meantime. Otherwise, water activities influence the basic electrochemical properties and induce material-dissolutions during functioning. Material pseudocapacitance is an alternative strategy to achieve faradaic electrodes of both high capacity and rate, where the intercalation pseudocapacitance is considered the most promising because of the full involvement of bulk reactions. In Chapter 4, the advantages of integrated intercalation pseudocapacitance and proton electrochemistry are disclosed, via the studies of proton redox chemistry in hexagonal MoO3 (h-MoO3). As a structure isomer to α-MoO3, similar properties can be found in h-MoO3 such as similar maximum proton exchange amount and an initial process out of structure rearrangements, etc. Interestingly, though surface ion de-solvation phenomena are also observed, it is identified increased crystal water in h-MoO3 after electrochemistry, which is attributed to certain hydronium intercalation into the intracrystalline tunnels. After the initial process, solid-solution proton intercalation is demonstrated in h-MoO3, accompanied with fast rate capabilities almost independent on particle sizes. Surprisingly, fast rate capabilities from proton intercalation pseudocapacitance has been demonstrated in electrodes of monocrystals over 100 μm scale. The high-potential MnO2/Mn2+ redox couple (MnO2 + 4H+ + 2e ↔ Mn2+ + 2H2O, Eθ=1.23 V, v.s. SHE) has recently attracted attentions in developing aqueous batteries, typically via electrodepositing solids on substrates for energy storage. This electrolysis reaction provides a facile and competitive cathode choice for the emerging proton batteries, because most of known electrodes either function at low potentials (due to proton reduction thermodynamics) or overlap in potentials with each other to restrict the cell voltage. However, its redox behavior is little understood in concentrated acids, and current full-cells often suffer limited cycle life (e.g., tens-of-hours). In Chapter 5, we show a homogeneous and stable MnO2 colloid electrolytes prepared by electrolysis in H2SO4 (≥ 1.0 M), and their application to achieve long life proton batteries. The colloid electrolytes enable prolonged cycling of a MnO2//MoO3 cell from 11.7 h to 33 days, and a MnO2//pyrene-4,5,9,10-tetraone cell for 489 days, which is the longest duration ever reported for proton batteries, to the best of the authors’ knowledge. Through water dilution colloids precipitate into hierarchical nanosheet spheres; Further characterizations together with deposited substrates reveal major electrolytic products as ε-MnO2 regardless of electrolytes. Colloids reform from precipitates differently with Mn2+ present/absent acids, suggesting colloid balances include both physical and chemical interactions. The results achieved in this thesis offer new fundamental insights in proton electrochemistry, introduce findings of novel electrodes and electrolytes, and demonstrate proof-of-concept application of proton batteries. The findings will guide the further search for electrode materials, exploitation of electrode performances, electrolytes, and advanced full-cell designs. It is my hope these would contribute to future energy storage techniques of high rate and capacity and beyond.

  • (2022) Qiao, Laicong
    Thesis
    There has been a rapid-growing market and academic enthusiasm for small wearable molecular diagnostic platforms driven by the growing demand for continuous monitoring of human health. Wearable devices need to be portable, stretchable, and ideally re-configurable to be able to work for different analytes. Such flexible physiological monitoring devices which are non-invasive or minimally-invasive represent the next frontier of biomedical diagnostics. They may make it possible to predict and prevent diseases or facilitate treatment by diagnosing diseases at the initial stages. However, there are many problems that restrict further applications of these devices. Firstly, there are a limited number of bio-materials which are highly flexible, biocompatible and have anti-fouling properties; such biomaterials are needed as substrates for wearable devices. Secondly, traditional biosensors used in wearable devices focus on the detection of physical signals (such as heartbeat) and small chemical molecules, e.g. Na+, K+. These are not sufficient to provide in depth health information which requires sensing of large molecules such as proteins, ideally in real time, which is currently challenging. This provides a motivation to develop highly sensitive wearable biosensors for the detection of large molecules in sweat. This thesis centres on the development of a bio-material based wearable device for continuous detection of crucial analytes in human sweat. To achieve this target, our first aim was to design a highly bio-compatible flexible material as a substrate for wearable devices. A tough and anti-fouling three-network hydrogel has been prepared by integrating a zwitterionic polymer network into a robust double-network hydrogel. Secondly, to fill the gap between technological development of continuous and non-invasive detection of different analytes in human sweat, a patterned sweat-based biosensor was created for the detection of key biomolecules. This sensor was produced by placing specific aptamers or enzymes on flexible working electrodes. In addition, nanotechnology methods have been applied to refine the bio-sensing interface to further increase the sensitivity of our sensors. Finally, a sample collection chip has been combined with our high sensitivity sensors to fabricate a wearable device for sweat bio-sensing purposes. Future research may involve integration of a commercially available wireless signal readout module with this wearable biosensing device. The outcomes of this work may provide new insights for the development of wearable devices for continuous measurement of a spectrum of analytes in sweat, as an important step towards point-of-care diagnostics

  • (2022) Li, Zihao
    Thesis
    Therapeutic proteins have long been considered difficult to mimic synthetically. While the chemistry to make very complex polymers is generally available, the tools to efficiently screen for the effect of a polymer’s structure on its biological activity have yet to be demonstrated. In this thesis, a high throughput platform was developed for the synthesis of multivalent polymer scaffolds and applied to design synthetic mimics of the chemotherapeutic protein, tumor necrosis factor related apoptosis inducing ligand (TRAIL), which triggers apoptosis by receptor clustering. The platform makes use of a simple dual-wavelength, two-step polymerise & click approach to prepare star-shaped polymer-peptide conjugates. Polymerisations were performed in open well plates at 565 nm using an oxygen tolerant porphyrin-catalysed photoinduced electron/energy transfer-reversible addition-fragmentation chain-transfer (PET-RAFT) process. Subsequent UV irradiation results in deprotection of the polymerisation friendly cyclopropenone-masked dibenzocyclooctyne (cp-DIBAC) group at the α-chain end and the click conjugation of the desired peptide. Using this approach, the valency and position of ligands on a polymer scaffold can be precisely controlled, in a high throughput manner, without purification. Leveraging this approach, libraries of star shaped polymers which present exactly one receptor binding peptide at the end of each arm were prepared and screened for their ability to bind to the target death receptor (DR5), and trigger apoptosis through receptor clustering. Structure-activity relationships generated on a colon cancer line (COLO205) led to the identification of ~ 10 kDa trivalent structures as the most promising leads, which showed IC50 values of ~ 2 µM. Elevated levels of caspase-8 were used to confirm the mechanism of cell death. The scaffold design was then iterated by introduction of hydrophobic blocks into the centre of the star polymer, which resulted in improved spatial control over peptide presentation in solution. This led to around 30-fold improvement in IC50 (75 nM). These results demonstrate the potential for high throughput methods in designing polymer mimics of complex therapeutic proteins, and offer promising leads in the development of better TRAIL-like agents, which are long expected as novel chemotherapies for cancer treatment.

  • (2022) Bennett, Jack
    Thesis
    The in-depth characterisation of protein–small molecule complexes is of paramount importance to both drug discovery and fundamental molecular biology. Understanding the structural and thermodynamic properties of such biomolecular assemblies can enable the rational development of new therapeutics, assist in the elucidation of protein function, or provide insights into the molecular mechanisms through which biological activity is regulated. Native mass spectrometry (MS) has emerged as a powerful tool for the investigation of protein–small molecule interactions within heterogenous biomolecular systems. Using native MS, numerous protein–small molecule complexes can be resolved in a single mass spectrum, allowing for the quantitative characterisation of multiple ligand binding events. This is in stark contrast to most established biophysical techniques, which are typically unable to characterise multiple protein–ligand interactions simultaneously. This thesis aims to explore proven applications of native MS in the study of protein–small molecule interactions, and to identify novel methods that facilitate the investigation of complex biochemical systems using such approaches. Chapter 1 provides a comprehensive review of the relevant literature, exploring the critical developments in MS instrumentation and methodologies that have enabled the high-resolution characterisation of protein–ligand complexes. Through a critical analysis of past investigations, the review outlines major challenges facing the field and suggests potential approaches for addressing many of these issues. The second chapter of this thesis outlines a novel native MS-based method for the direct identification of protein–ligand complexes formed from natural extracts containing more than 5,000 potential small-molecule binders. Using this approach, several novel ligands of a key human drug target are identified. Improvements in method efficiency are subsequently made to ensure that the approach could be employed for large-scale pharmaceutical screening campaigns or used for the elucidation of novel interactions between protein complexes and endogenous metabolites. Finally, chapter three aims to identify novel chemical additives that can reduce the charge of protein–ligand complexes in native MS. Charge-reducing agents for positive-mode native MS have been previously shown to facilitate accurate quantitative analysis of protein–small molecule interactions, by increasing the kinetic stability of the gas-phase ions. In this chapter the author explores the properties of several chemical agents that reduce the charge of anionic protein complexes. The effect of these agents on the charge state of various model proteins is characterised to critically evaluate their analytical utility. Furthermore, their effect on the gas-phase stability of a labile protein–ligand complex is also explored. Such agents may prove useful in the quantification of weak interactions that cannot be accurately characterised using standard native MS-based approaches.

  • (2022) Pointing, Lewis
    Thesis
    Wastewater processing conditions in manufacturing environments often involve the three key factors for optimum bacterial growth - water, ideal temperature, and a constant food source. Bacteria are problematic because they can reduce product yield by consuming product and metabolise it into organic acids which lower the process pH, requiring large amounts of chemicals to control. At a casestudy wastewater treatment plant, a site-wide analysis of the impacts of chemical sanitation methods had not been conducted and the efficacy of these chemicals had not been established. To understand the impacts of current sanitation practices, standard microbiological plating techniques combined with HPLC testing to measure lactic acid as a proxy for microbial activity were used. Nitrogensource determination and solids analysis were used extensively to provide a comprehensive picture of the stream properties throughout the plant. I show that current microbial control methods are ineffective for significantly limiting microbial growth in the water treatment plant. The most important factors impacting this are the concentration of nitrogen-sources followed by total organic solids at chemical dosing sites, which react more rapidly with oxidative sanitisers than bacteria do. These findings indicate that chemical sanitisers would be more effective if dosed in locations with minimal concentrations of nitrogen-sources and organic solids. In practice, this is difficult to achieve in an existing plant without significant capital expenditure and so investigation of alternative, nonchemical methods of sanitation in combination with more effective use of chemical methods is recommended.

  • (2022) Yu, Tsz Tin
    Thesis
    The rapid emergence and development of antibacterial resistance is a major global threat to public health. There is an urgent need for the development of antibacterial agents with novel therapeutic strategy to tackle the increasing incidence of antibacterial resistance. In recent years, antimicrobial peptides (AMPs) and their synthetic mimics have been under the spotlight of the development of a novel class of antibiotics to combat antibiotic resistance. This research project focused on the utilisation of phenylglyoxamide and benzothiazole scaffolds in the development of antimicrobial peptidomimetics. The synthesis of phenylglyoxamide-based peptidomimetics was achieved via the ring-opening reactions of N-sulfonylisatins with primary amines followed by salt formation. Minimum inhibitory concentrations (MIC) of the peptidomimetics against different bacterial strains were determined to assess their antibacterial activity. Structure-activity relationship (SAR) studies revealed the inverse relationship between the alkylsulfonyl chain length and the bulkiness of the phenyl ring system for high antibacterial activity. The most active peptidomimetics exhibited high antibacterial activity with the lowest MIC to be 4, 16 and 63 μM against S. aureus, E. coli and P. aeruginosa, respectively. These peptidomimetics also showed significant biofilm disruption (up to 50%) and inhibition (up to 70%) against S. aureus at 2–4× MIC. In addition, terphenylglyoxamide-based peptidomimetics synthesised by the ring-opening reaction of N-acylisatins with amines and amino acid esters were evaluated for their quorum sensing inhibition (QSI) activity against P. aeruginosa MH602. The most potent peptidomimetic possessed high QSI activity of 82%, 65% and 53% at 250, 125 and 62.5 μM, respectively, with no bacterial growth inhibition. On the other hand, benzothiazole-based peptidomimetics were synthesised via the Jacobson method of cyclisation of phenylthioamides, followed by the installation of cationic groups. 2-Naphthyl and guanidinium hydrochloride as the hydrophobic and cationic groups, respectively, were important for high antibacterial activity of the peptidomimetics against both Gram-positive and Gram-negative bacteria. The most potent peptidomimetics against S. aureus, E. coli and P. aeruginosa possessed MIC values of 2, 16 and 32 μM, respectively. These active peptidomimetics inhibited 39% of S. aureus biofilm formation and disrupted 42% of preformed S. aureus biofilms at sub-MIC.

  • (2022) Gadde, Satyanarayana
    Thesis
    High-risk neuroblastoma is one of the most aggressive and treatment-refractory childhood malignancies. MYCN (v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived) is a major oncogenic driver for neuroblastoma (NB) tumorigenesis. Developing direct inhibitors of MYCN has been challenging due to several limitations. Hence, targeting MYCN-binding proteins which regulate the stability of MYCN protein is a promising alternative approach. This study is aimed at developing novel inhibitors of ubiquitin specific protease 5 (USP5), a deubiquitinating enzyme, which is known to prevent MYCN protein degradation by deubiquitination. The first results chapter describes the synthesis of novel pyrido[1,2-a]benzimidazole compounds and their cytotoxicity against MYCN amplified NB cells with high expression of USP5 protein (SK-N-BE(2)-C and Kelly cells). However, none of the tested compounds displayed better cytotoxicity than the parental compound, SE486-11. The second results chapter describes a one-pot synthesis of novel γ-carbolinone, γ-carboline and spiro[pyrrolidinone-3,3′]indoles. One of the γ-carboline compounds (42d) displayed promising cytotoxicity against NB cells (SK-N-BE(2)-C (IC50 = 1.21 μM) and Kelly (IC50 = 3.09 μM)) but showed little therapeutic selectivity when compared to normal human fibroblasts, MRC-5 cells (IC50 = 3.75μM). The synthesis and cytotoxicity of novel pyrimido[1,2-a]benzimidazoles is described in the third results chapter. The active compound, 65a displayed promising cytotoxicity against SK-N-BE(2)-C (IC50 = 0.78 μM) and Kelly (IC50 = 2.00 μM) cells with a reasonable therapeutic window compared to MRC-5 cells (IC50 = 15.0 μM). 65a bound to USP5 protein by microscale thermophoresis assay (Kd = 0.47 µM). USP5 and MYCN protein levels were decreased in NB cells by treatment with 65a. Moreover, the cytotoxicity of 65a was dependant on the expression of USP5 and MYCN proteins. 65a showed synergy in combination with HDAC inhibitors, SAHA and panobinostat. In the fourth results chapter, the synthesis of more potent pyrimido[1,2-a]benzimidazoles with di- and tri- substitutions on the pendant phenyl ring (86b (SK-N-BE(2)-C IC50 = 0.31 μM; Kelly IC50 = 0.65 μM) and 91 (SK-N-BE(2)-C IC50 = 0.03 μM; Kelly IC50 = 0.07 μM)) are described. Importantly, 86b displayed significant in vivo efficacy in TH-MYCN homozygous NB mice when treated with 60 mg/kg for three weeks. The last results chapter describes the synthesis and cytotoxicity of novel benzo[4,5]imidazo[2,1-b]thiazole and pyrido[2,3-b]indole compounds. Collectively, this thesis identifies promising novel scaffolds with great potential for further development.