Medicine & Health

Publication Search Results

Now showing 1 - 10 of 50
  • (2021) Peng, Wang
    Thesis
    The HIV-1 capsid interacts with mutiple host factors during its early life cycle to achieve succesfful infection. In this thesis we aim to expand our understanding of how interactions between the capsid and host cell factors regulate viral activities, with chapter 4 and 5 specifically focusing on the cytoplasmic transport process. Based on cellular and biochemical evidence, recent studies suggest that HIV-1 capsid hijacks both dynein and kinesin-1, via the adaptor proteins BICD2 and FEZ1 respectively, for active transport along microtubule network. We will present our work to reconstitute these complexes and demonstrate their motilities along microtubles in vitro, providing more direct evidence to support these models. To investigate the interactions between HIV-1 capsid and the motor adaptors, we applied a fluorescence fluctuation spectroscopy based binding assay and a total internal reflection microscopy (TIRFm) based binding assay. These approaches allowed us to generate quantitative descriptions of the interactions between HIV-1 capsid and the adaptor proteins. Subsequently, we reconstituted the motor-adaptor-cargo complexes (DDBC and KFC) using recombinant proteins as well as components isolated from native tissues. We have successfully demonstrated both the dynein- and kinesin-dependent transport of HIV-1 capsid along microtubules in vitro using a TIRFm based single molecule motility assay. We also further charaterized the motile behaviors and properties of the KFC complex. Our work validated the proposed models for the cytoplasmic transport of HIV-1 capsid and demonstrated the minimum requirement for this process. In general, this work has made solid contributions towards the understanding both HIV viology and motor-driven cargo transport, as well as opened oppotutnities to a range of exciting research questions in both fields.

  • (2021) Begik, Oguzhan
    Thesis
    RNA modifications, collectively referred to as the ‘epitranscriptome’, are not mere decorations of RNA molecules, but can be dynamically regulated upon environmental queues and changes in cellular conditions. This dynamic behaviour is achieved through the RNA modification machinery, which comprises “writer”, “reader” and “eraser” proteins that modify, recognize and remove the modification, respectively. Chapter1 presents a comprehensive analysis of the RNA modification machinery (readers, writers and erasers) across species, tissues and cancer types, revealing gene duplications during eukaryotic evolution, changes in substrate specificity and tissue- and cancer-specific expression patterns. Chapters 2 and 3 presents the exploration and development of novel methods to map and analyze RNA modifications transcriptome-wide. Nanopore direct-RNA sequencing technology was used to provide RNA modification maps in full-length native RNA molecules. Firstly, it is shown that RNA modifications can be detected in the form of base-calling ‘errors’, thus allowing us to train Support Vector Machine models that can distinguish m6A-modified from unmodified sites, both in vitro and in vivo. Secondly, it is demonstrated that distinct RNA modification types have unique base-calling ‘error’ signatures, allowing us to exploit these signatures to distinguish different RNA modification types. It is found that pseudouridine has one of the most distinct signatures, appearing in the form of C-to-U mismatches. Finally, this information was used to predict novel pseudouridine sites on ncRNAs and mRNAs transcriptome-wide, as well as to obtain quantitative measurements of the stoichiometry of modified sites. Chapter 4 presents the development of a novel nanopore-based method, which is termed ‘Nano3P-seq’, to simultaneously quantify RNA abundance and tail length dynamics in individual molecules in both the coding and non-coding transcriptome, from cDNA reads. It is demonstrated that Nano3P-seq offers a simple approach to study the coding and non-coding transcriptome at single molecule resolution regardless of the tail ends. Together, this work provides a comprehensive framework for the study of RNA modifications and polyA tail dynamics using third generation sequencing technologies, opening novel avenues for future works that aim to characterize their dynamics and biological roles both in health and in disease.

  • (2021) Ross, Samuel
    Thesis
    Upon fertilisation of vertebrate embryos, the epigenomes of the responsible gametes need to be reconfigured into a state that is compatible with totipotency and zygotic transcriptional programs. Furthermore, the epigenomes of differentiating cells then need to be remodelled again in order to form the complex structures of the body, such as the vastly intricate nervous system. This includes, but is not limited to, the remodelling of DNA methylation, the most abundant DNA modification in vertebrates with critical roles in embryogenesis and neurodevelopment. In mammals, methylation of cytosines in cytosine-guanine dinucleotides (mCG) is almost completely erased after fertilization before it is re-established during gastrulation. Similarly, methylation of cytosines outside the CG context (mCH; H = A,T,C) is diluted in the early mammalian embryo before it is re-established mainly in the nervous system. However, in non-mammalian vertebrates, it appears that no global erasure of mCG takes place, raising questions about their propensity for transgenerational epigenetic inheritance. Additionally, the conservation of mCH in non-mammalian vertebrates is largely unexplored. In this thesis, I look to expand our knowledge on the developmental dynamics, evolutionary conservation and the molecular components of DNA methylome remodelling in vertebrates by studying methylome dynamics in two distantly related teleost species (ray-finned, protruding jawed fish). I functionally explore how DNA methylation is regulated during the development of zebrafish (Danio rerio), medaka (Oryzias latipes), and zebrafish-medaka hybrids, in both the CG and CH context. I employ CRISPR/cas9 technology, whole-genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and RNA sequencing (RNA-seq), to interrogate a wide range of developmental time points and adult tissues. Overall, I have: i) developed a system to functionally test for regulators of developmental DNA methylation; ii) revealed a novel form of developmentally remodelled mCH in zebrafish and medaka which is deposited by the teleost specific DNMT3BA enzyme, iii) demonstrated evolutionary conservation of mammalian-like mCH features in the developing zebrafish nervous system, and iv) shown that DNA methylome dynamics in medaka and zebrafish embryos are highly comparable and compatible during the first 24 hours of zebrafish-medaka hybrid development. Altogether, this work greatly expands our understanding of the form and function of a critical DNA modification during development.

  • (2021) Chilver, Miranda
    Thesis
    Mental wellbeing, a state of positive subjective experience and psychological functioning, is a key component of mental health. Despite this, little is known about how mental wellbeing is manifested in the brain, or how such neural associations covary with depression and anxiety symptoms. Thus, the aim of this thesis was to explore potential electrophysiological markers of wellbeing using electroencephalography (EEG) and event-related potentials (ERPs). To facilitate further investigation into the association between electrophysiology and wellbeing, a positive psychology intervention was also developed. Following an introduction to the key topics, Chapter 2 examined the relationship between mental wellbeing and resting EEG power. This study identified a specific profile of resting EEG power that is associated with wellbeing, independent from depression and anxiety symptoms. Twin modelling clarified that this EEG profile shares a genetic correlation with mental wellbeing. Chapters 3 and 4 shift towards using ERPs to investigate how wellbeing and depression and anxiety symptoms are associated with emotional and cognitive processing. Chapter 3 reported that wellbeing was not significantly associated with emotion processing after accounting for depression and anxiety symptoms, which were significantly associated with alterations in emotion processing. In Chapter 4, no evidence was found for an association between wellbeing or depression and anxiety symptoms with cognitive ERPs, although associations with behavioural performance reported in previous studies were replicated. Finally, Chapter 5 reports on the effectiveness of an online positive psychology intervention which was found to significantly improve wellbeing, particularly subjective wellbeing. Although COVID-19 restrictions prevented the evaluation of causal links between wellbeing and EEG using this intervention, it is discussed for purposes of future research. Together, this thesis provides one of the first investigations into the electrophysiological correlates of mental wellbeing. Resting EEG power was identified as the most promising avenue for future research aiming to establish endophenotype markers of mental wellbeing, with the task-related measures assessed here were not associated with wellbeing. A short and effective online intervention was developed that could be used to facilitate future investigations into the use of resting EEG as a predictor and marker of mental wellbeing.

  • (2022) Forest, Chelsea
    Thesis
    In the last 40 years there have been many strides taken towards better and more selective cancer treatment using nanoparticles. Nanoparticles can have inherent passive accumulation in tumour cells, known as the enhanced permeability and retention effect (EPR) which makes them a strong therapy candidate; however this effect is not as well defined or effective as once thought. There is a large variance of efficacy between different patients due to the heterogeneity of tumours, therefore a more targeted nanoparticle systems needs to be designed to increase selectivity and efficacy. This thesis describes the design, synthesis, and characterisation of 20 novel ellipsoidal polymersomes decorated with peptide ligands for selective targeting of medulloblastoma, a childhood brain cancer. These ligands were FSRPAFL 1 a medulloblastoma cell targeting peptide and T7 26 a transferrin targeting peptide designed to aid in crossing the blood brain barrier (BBB). A new synthetic method was designed to attach the peptide ligands post self-assembly, so the peptides were attached to the hydrophilic corona rather than the hydrophobic membrane of the polymersomes. Analysis of these polymersomes showed more ligand available for binding but this did not translate to increased cell association due to an over saturation of ligand. The ratio and density of the targeting peptide 1 and BBB peptide 26 was altered on the surface of the polymersomes and it was found that the polymersomes with 100% T7 ligand showed rapid and high cell association with two different subtypes of SHH medulloblastoma (DAOY and UW228) as well as high association with brain endothelial cells that make up the BBB (HBEC-5i) making it a promising candidate as a drug delivery system for SSH medulloblastoma. Finally, linearly conjugated dual peptides made up of both targeting peptide 1 and T7 peptide 26 sequence, were synthesised and attached to the polymersome hydrophilic corona and analysed against the non-conjugated dual-functionalised peptide polymersomes. There was no significant difference between the two ligand conjugation method analysed but further research should be conducted to confirm this. The work described in this Thesis has shed light on the multitude of nuances that make up the composition of mono and dual functionalised peptide nanoparticle systems and how these can influence biological function. Future work will allow for a better understanding of fundamental questions about targeted nanoparticles therapies and how ligand characteristics directly impact biological function, selectivity and efficacy.

  • (2022) Biswas, Raaj Kishore
    Thesis
    Rear-end crashes are a major part of road injury burden, accounting for one-third of all vehicle-to-vehicle crashes in New South Wales, Australia. Close following or driving with short headways is a key cause, yet the role of driver behaviour in rear-end crash risk is not well researched. The primary aim of this research was to develop a better understanding of rear-end crashes by assessing headways on Australian roads and investigating driver behaviour and performance associated with close following in crash and non-crash scenarios. Two systematic reviews of headway were conducted. First, a review of research on headway identified the need for a consistent and accurate definition of headway, so the thesis puts forward an improved definition. The second review identified the range of external factors that increase the risk of short headway and increase crash risk including speed, task engagement, lead vehicle type, traffic conditions, road characteristics, weather/visibility, drug use, driving fatigue, innovative lane markings, and various warning systems. These factors were then explored in New South Wales data on rear-end casualty and multiple vehicle crashes. The modelling of these associated factors were confirmed as contributing factors in rear-end crashes, congruent with the review of headway. Higher speed, free flowing traffic, volitional task engagement, low cue environments, and collision warning lead to longer headway. Despite lower fatalities, higher odds of injury were observed for rear-end crashes than other crash types. Rear-end crashes were more likely to lead to multiple vehicle crashes, which had a higher chance of fatality than other types of crashes. Finally, naturalistic driving study data was used to investigate headway during normal driving, exploring close following at different speeds and classifying potential risky driving at various headways. In 64 hrs accumulated across 2101 trips, short headways of under 1 s occurred in around 15% of driving. Common manoeuvres to avoid rear-end crashes when close following were changing lanes, or braking, almost always by the following driver. Headway was associated with both driver speed and posted speed limits, decreasing as posted speed limits increased. Over-the-speed-limit driving was observed in all headway scenarios, but especially in higher speed zones. The findings challenge the notion that rear-end crashes are less severe with low injuries. Road users should be made aware of how frequently safe headways are violated and severity of injury outcomes. Driver education, community engagement, application of driver assistance technology consistent with driver behaviour and safety campaigns need to focus on safer speed and headway management to reduce rear-end crash risk.

  • (2022) Sloane, Jennifer
    Thesis
    From a child interrupting a conversation between her parents to ask "What's for dinner?" to a nurse interrupting a physician in the middle of a complex procedure with an urgent message, interruptions are an inevitable part of our daily lives no matter who we are, where we live, or what we do. Interruptions can have a variety of affects on people's performance and behavior. While interruptions may sometimes facilitate performance, often interruptions have negative consequences. For example, interruptions may result in people making more errors or forgetting to complete a prior task altogether. This thesis examines existing strategies to help mitigate interruption costs and explores the effects of interruptions within different decision environments. Chapter I introduces the topic by discussing a few theoretical frameworks of interruptions and reviewing prior research on what makes interruptions disruptive. One strategy to minimize interruption costs is to use what is called an interruption lag, which can be thought of as taking time to prepare for a pending interruption. Chapter II presents a novel experiment to systematically explore the potential benefits of interruptions lags and an alternative intervention (i.e. providing feedback) when interruption lags are not possible. Chapters III and IV discuss the results from three experiments and a final replication study that all focus on how interruptions affect people's decision making in unique environments. The environments consist of easy problems (i.e. basic arithmetic problems) and trick problems, designed in such a way to lead the reader down an incorrect path. Results from these studies were mixed. While there was some evidence that interruptions may make people more susceptible to falling for the trick answer, this finding was inconsistent across all the experiments. Chapter V applies the findings from the previous chapters to a medical context. This chapter presents novel medical cases that were developed with the help of a medical expert. These cases consisted of easy, hard, and trick cases designed for medical students. The goals of this chapter were to validate the cases and to investigate the effects of interruptions within the different case types. The final chapter (Chapter VI) concludes with a general discussion of the experimental findings, the theoretical implications of the results, and the broader implications of this research for the field of medicine.

  • (2022) Jamshidi, Javad
    Thesis
    Wellbeing, a key aspect of mental health, is defined as a state of positive subjective experience and optimal psychological functioning. This thesis presents a series of studies devised to comprehensively explore phenotypic, genetic, and neural correlates of wellbeing. The first study (Chapter 2) aimed to compare the heritability and stability of different wellbeing measures in the TWIN-E dataset (N~1600) to discern the most suitable approach for measuring wellbeing for subsequent gene discovery efforts. This twin-based study concluded that multi-item measures of wellbeing such as the COMPAS-W scale, were more heritable and stable than single-item measures. Wellbeing-associated variants were identified via genome-wide association studies (GWAS) and highlighted the need for larger sample size. The subsequent studies were conducted using population-scale data from the UK Biobank comprising ~130,000 participants with phenotypic and genetic data. Thus, in Chapter 3, I constructed a multi-item “wellbeing index” measure using UK Biobank data to investigate its relationship phenotypically and genetically (using GWAS, polygenic scores and LD score regression) with negative mental health indicators (e.g., neuroticism and loneliness), childhood maltreatment and psychiatric illness. I confirmed that SNP-heritability of wellbeing index was higher than both single-item measures and estimates previously reported (SNP-h2 = 8.6%). Moreover, I provide an overview of phenotypic and genetic correlations between wellbeing index and negative mental health indicators. In addition, childhood maltreatment and psychiatric illnesses were associated with reduced wellbeing, with evidence that genetic factors may influence their correlations. In Chapter 4, I investigated the genetic and phenotypic associations between wellbeing index and brain structure, using magnetic resonance image-derived phenotypes from the UK Biobank. This study found associations between wellbeing and volumes of brainstem, cerebellum and subcortical regions, and structural morphology of various cortical regions. Thus, wellbeing is associated with complex structural variations, each with a small effect. Together, this thesis explores the multifaceted nature of wellbeing, elucidating its phenotypic and genetic relationships with related phenotypes, childhood maltreatment, and psychiatric outcomes, and provides novel insights into the associations between wellbeing, its genetic signatures and brain structure.

  • (2022) Bhattacharjee, Shovon
    Thesis
    There is an ongoing global threat of highly transmissible infectious disease outbreaks such as the COVID-19 pandemic. Consequently, the demand for effective, sustainable, and reusable personal protective equipment (PPE) is high for the protection of the frontline workers and community, especially with possible vaccine-resistant variants emerging. However, the commonly used PPE, especially protective clothing, and face masks, has several drawbacks and improvement areas. In this thesis, three state-of-the-art reviews (Chapters 2A, 2B, and 2C) identified the challenges and limitations of commonly used protective clothing and face masks. Potential new materials, technologies, and strategies were also addressed to overcome the limitations and challenges. Lastresort strategies were outlined to help people navigate their choices during mask shortages. In addition, it was revealed that the multifunctional performance of PPE could be significantly enhanced with the application of advanced materials such as graphene and metal nanoparticles (NPs). Accordingly, in Chapters 3 and 4, reduced graphene oxide (RGO) and copper (Cu)/silver (Ag) NPs incorporated cotton and silk fabrics were developed by a facile dip and dry method using a silane crosslinking agent followed by chemical reduction and vacuum heat treatment. The developed fabrics demonstrated excellent multifunctional activities such as hydrophobicity, electroconductivity, Joule heating capacity, heat dissipation, thermal stability, mechanical stability, UV shielding, and washing durability. Especially, the RGO- and Cu-NPs-embedded cotton and silk fabrics exhibited the best multifunctional performances with high washing durability among all other fabric samples. To further assess the potential of protective clothing, antimicrobial activity and biocompatibility of the developed fabrics were investigated in Chapter 5. The graphene and Cu/Ag NPs incorporated fabrics showed excellent activity against bacteria (Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus) and fungus (Candida albicans). On top of the antimicrobial activity, the developed fabrics showed low cytotoxicity, making them a potential candidate for application in next-generation PPE. During COVID-19, due to the massive global shortage of disposable masks/respirators, cloth masks became a mainstay and showed hope of being a sustainable alternative to medical masks. Chapter 6 provides a comprehensive study using violent respiratory events (sneeze) and evaluating all dimensions of protection (respiratory droplet blocking efficiency, water resistance, and breathing resistance) to develop a blueprint for the optimal design of a high-performing reusable cloth mask that can outperform a disposable surgical mask. The results reveal that droplet blocking efficiency increases by ∼20 times per additional fabric layer. A minimum of 3 layers with a combination of cotton/linen (hydrophilic) for the inner layer, blends for the middle–layer, and polyester/nylon (hydrophobic) for the outer–layer is required to resemble the performance of surgical masks. The fabrics' average thread count and porosity should be greater than 200 and less than 2 %, respectively. Overall, the developed graphene/NPs incorporated multifunctional fabrics, and face mask design proved to be a breakthrough to prevail over the limitations of the conventional PPE materials. They hold great promise to be applied to a broader range of PPE and could provide a sustainable PPE solution globally.

  • (2022) Shvetcov, Artur
    Thesis
    Rodents learn to fear a stimulus (e.g., a light) that signals the imminent arrival of an innate source of danger (typically an aversive foot shock). They also learn to fear a stimulus (e.g., a noise) that signals a learned source of danger (e.g., the already conditioned fear-eliciting light). Following Pavlov (1927), the former type of fear is termed first-order conditioned fear, because the stimulus is paired with an aversive unconditioned stimulus (US). The latter is termed second-order conditioned fear, because the stimulus is paired, not with a US, but with an already conditioned stimulus. There are both commonalities and differences in the neural substrates underlying these two forms of fear. Both require neuronal activity in the basolateral amygdala complex (BLA), including activation of NMDA receptors, for their encoding, and both require CaMK signalling, gene expression and DNA methylation for their consolidation. However, de novo protein synthesis is required for consolidation of first-order fear but not for consolidation of second-order fear.