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(2022) Qiao, LaicongThesisThere 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
(2023) Wimberger, LauraThesisThis work explores how reversible light-induced pH changes can be increased and applied to control pH-responsive systems with light. Chapter 2 investigates how substitution patterns influence the acidity of merocyanine photoacids in the dark as well as under light irradiation. The parameters which are crucial for increasing light-induced pH changes are defined and applied to synthesized merocyanine photoacids. The light-induced pH changes starting from varying initial pH values are explored and a model is developed to estimate these based on experimentally defined parameters. Transient absorption spectroscopy was used to explore the influence of the protonation state of the merocyanine form (MCH vs MC) on the photoswitching efficiency. A python model is developed to describe the pH- recovery in the dark. Chapter 3 introduces an improved merocyanine photoacid, designed by principles outlined in Chapter 2. The acidity parameters and photoswitching abilities are characterized. The pH switching capacity is investigated and extended into the basic pH range. The light-induced pH switch by the improved photoacid is applied to control the protonation state of an indicator dye. Chapter 4 applies light-induced pH changes to influence the secondary structure of pH-sensitive DNA. The transient formation of these structures is explored. The influence of the initial pH value and a DNA binder on the ratio and kinetics of the system components is investigated. Chapter 5 applies light-induced pH changes to influence the properties of different types of supramolecular polymers. The challenges of applying merocyanine photoacids to generate structural changes of supramolecular polymers by influencing the components protonation state are highlighted. Chapter 6 presents brief conclusions and a future outlook for this research field.
(2023) Zhang, DianaThesisEarly disease diagnosis can significantly improve patient survival rates as appropriate treatment strategies can be timely administered. A promising approach for disease diagnosis is to analyse chemical biomarkers present in bodily fluids as these molecules can provide insights into human metabolic and physiological processes. Changes in the identity and concentrations of such chemicals can help distinguish healthy from disease states. However, some current methods used to collect, analyse, and identify these chemicals have been challenged by limitations in sampling protocols, the resolving power of instruments, and the ability to interpret advanced data analysis methods. This thesis comprises of five concurrent efforts to enhance diagnostic accuracy by investigating various machine learning and analytical approaches. Firstly, an interpretable machine learning framework for binary disease classification is presented. Using this framework on blood plasma and skin sebum data, the diagnostic performance for Parkinson’s disease and key disease biomarkers are reported. Secondly, a protocol and recommendations for robust skin sebum analysis is described. Following a semi-longitudinal study, the various factors that can impact the collection and detection of volatile organic compounds present in skin sebum is discussed. Thirdly, the clinical utility of high-field asymmetric waveform ion mobility spectrometry (FAIMS) for disease diagnosis is reported. Based on a systematic review and meta-analysis, the diagnostic accuracy and clinical implications of using FAIMS is discussed. Fourthly, the performance of high-resolution FAIMS resulting in enhanced ion separations is reported. Using high-resolution FAIMS, the fundamentals that govern the separation of protonation protein isomers is described. Finally, the use of high-resolution FAIMS to analyse volatile organic compounds present in exhaled breath is demonstrated. Using atmospheric pressure chemical ionisation coupled with high-resolution FAIMS, untargeted breath analysis on individual breath profiles is reported. Overall, by improving analytical and machine learning methods, these findings should increase diagnostic accuracy and enable greater confidence in biomarker analysis.
Stimuli-responsive Nanoparticles for Drug Delivery and Novel Acetylcholinesterase Inhibitors and their Use as Protease Sensors(2023) Kaltbeitzel, JonasThesisProteins and enzymes are highly versatile materials that are involved in essentially every biological process, making them valuable tools and targets in the field of medicine. This thesis explores two distinct aspects of their applications: Part I focuses on the formation of responsive nanoparticles for drug delivery, while Part II delves into the development of small molecular inhibitors and their use in a novel protease assay. Each part will start with a separate literature review, to give the reader a brief background about the topic. Their biocompatibility, non-toxicity, and ability to specifically interact with cellular receptors make proteins and enzymes promising materials in the design of nanoparticles for drug-delivery applications. In many cases, a covalent modification of the protein is required to drive the formation of nanoparticles which can inadvertently change the properties of the underlying protein. One possibility to overcome this problem is to make the covalent modification reversible by the introduction of responsive linker molecules, which additionally allows targeting. Therefore, Part I of this thesis will explore nanoparticles that degrade in response to specific environmental cues, such as reducing agents, UV-light, or hypoxia. The first chapter is a comprehensive review of the literature on different protein-nanoparticle and the use of responsive linker systems in drug delivery applications. Chapter 2 of the thesis will present the synthesis of PEGylated enzyme nanoparticles designed for delivering catalytically active enzymes into cells. The results obtained will demonstrate the triggered disassembly of the nanoparticles and the subsequent release of catalytically active enzymes, leading to cellular toxicity. Moving on to Chapters 3 and 4, reductive-responsive nanoparticles composed of bovine serum albumin (BSA) and a hypoxia-responsive polymer will be featured as an intracellular drug delivery vehicle for nucleic acids. In Part II of the thesis, the focus is shifted to the design of small molecule inhibitors for acetylcholinesterase (AChE) and their use in the development of a novel protease assay. AChE has important implications in the treatment of Alzheimer's and other diseases. After a short literature review in Chapter 5 discussing the enzyme and past development of its inhibitors, Chapter 6 shows the journey in the design of potent, primary amine-containing inhibitors of AChE based on several known scaffolds. The increased polarity of the molecules hinders their ability to cross the blood-brain barrier, suggesting a potential application in the treatment of functional dyspepsia. Lastly, Chapter 7 deals with the development of a new proteases assay based on the inhibitors synthesized in the previous chapter. Proteases play a crucial role in many biological processes and are thus important medical markers for various diseases. The effect of the potency of the inhibitors after covalent modification with short peptides was evaluated and a mathematical model developed to predict the sensitivity of the assay.
(2023) Islam, Md SharifulThesisTissue engineering aims to create functional tissues by cultivating cells in a laboratory setting. A primary area of focus to achieve that objective is the development of scaffolds capable of providing a suitable environment for cellular adhesion, growth, and the execution of fundamental cellular functions to establish tissue-scale properties. However, scaffold systems in the laboratory do not benefit from the dynamic forces that are exerted on tissues in an organism. In pursuit of this aim, the overall objective of this thesis was to develop a tissue engineering scaffold system mimicking the natural tissue-like environment, with in-built capabilities for external control of dynamic mechanical properties to modulate cell differentiation. We first developed a magnetic nanoparticle-loaded hydrogel system, where the modulus of the hydrogels can be reversibly altered by applying a magnetic field. To demonstrate versatility, we have used two popular hydrogel systems broadly used in tissue engineering: poly (ethylene glycol dimethacrylate) and gelatine methacryloyl. We analysed the effects of the field-induced change in stiffness on cell behaviour upon the attenuation of a magnetic field. Our studies demonstrate that adipose-derived stem cells (ADSC) and embryonic muscle cells (C2C12 cell line) can perceive these stiffness changes and differentiate towards myofibroblast and myoblast, respectively. We then developed a composite hydrogel system to segregate the magnetic particles within gelatin fibres, which simultaneously provides nanotopography to the adherent cells. We used electrospinning to synthesize magnetic gelatin nanofibers containing 5 wt/v% iron oxide nanoparticles. This concentration was selected to ensure maintenance of fiber morphology while simultaneously ensuring magnetic response. To stabilize the nanofiber structure, we used a crosslinking method involving citric acid and high temperature to stabilize the gelatin via amide bonds between strands. Introducing a magnetic nanofiber mat at the interface of the hydrogel system provides remote actuation of the nanotopography through an external magnetic field. We found that the nanotopography alone directed adipogenesis, while mechanical actuation of the interface drove osteogenesis in adherent ADSCs. The adhesion characteristics suggest that the field influences the nanofiber structure, greatly enhancing focal adhesion. The field induced actuation was also found to stimulate the formation of aligned multinucleated myotubes and markers associated with maturation in adherent C2C12. Finally, we integrated the magnetic nanofiber into hydrogels as a modular system that closely resembles the fibrous network in the natural extracellular matrix. These hydrogels can be reversibly stiffened in response to external magnetic fields within cell-laden 3D constructs. Including a small fraction of short nanofibers (<3%) can significantly influence ADSC and C2C12 differentiation. As before, nanotopography was beneficial to adipogenesis while stiffening promoted enhanced osteogenesis and myogenesis. Together, this body of work provides a modular platform with broad versatility in format to study the effects of nano-topography and dynamic mechanics in cell systems. Moreover, these hydrogels and the magnetic components are cytocompatible with scope for inclusion in tissue bioreactors as a means for dynamic stimulation of cell differentiation for tissue engineering.
(2024) Han, ZifeiThesisReceptor clustering is one of the most common mechanisms for controlling cell fate in nature, and strategies capable of directing this behaviour hold significant therapeutic potential. One prominent example is the TRAIL protein (TNF-related apoptosis inducing ligand), which selectively induces apoptosis in cancer cells by clustering death receptors DR4 and DR5. Although a potent chemotherapeutic, its clinical use has been hampered by its short circulation half-life. In this thesis, multivalent polymer scaffolds capable of presenting DR4/5 binding peptide ligands were developed as synthetic TRAIL mimics. In any synthetic protein mimic, directing the conformational structure to precisely control the spacing and orientation of multiple ligands is a major challenge. The two scaffolds in this thesis applied different strategies to achieve this. The first scaffold was a core-crosslinked micelle system with surface functionality for attachment of DR5 binding peptides. Micelles featuring varying peptide densities were synthesized and carefully characterized. These micelles successfully induce apoptosis in a colon cancer cell line (COLO205) via DR5 clustering. Micelles with a peptide density of 15% (roughly 1 peptide / 45 nm2) displayed the strongest activity with an IC50 value of 0.8 μM (relative to peptide), suggesting a statistical network of monomeric ligands may suffice to drive DR4/5 signalling. However, significantly improved activity could be achieved using star polymers with a hydrophobic core. Structural characterization by DOSY-NMR and surface plasmon resonance revealed that the improved activity came from the polymer folding in solution, which positioned the peptides in a well-defined manner on the periphery of the star, enhancing their accessibility to DR5. By varying the chemistry of the inner block, a new lead structure of 3-arm PBzA40-b-PDMA40-WDCL was identified in library screening with IC50 values in the low nanomolar range to COLO205. These leads show toxicities approaching that of the native TRAIL protein, but from a material that would be expected to show upwards of 20 h circulation half-lives in vivo.