Minerva Elements Records
Permanent URI for this collection
Search Results
1 - 10 of 2066
-
ItemRNA stability in alphavirus infected cells( 2022-04)Alphavirus is a genus of viruses in the family Togaviridae. Alphaviruses include notable human pathogens such as Chikungunya virus (CHIKV), which causes arthritis, and the equine encephalitis viruses, which cause encephalomyelitis. The only alphavirus vaccine approved for human use is the Ixchiq vaccine for CHIKV, approved in late 2023. Alphaviruses subvert many processes of host cells to facilitate their own replication and evade the immune response. By understanding these host-pathogen interactions, treatments can be potentially targeted towards these host processes on which the alphaviruses depend for replication. Preliminary data from the Fazakerley lab shows that the alphavirus Semliki Forest virus (SFV) replicates less efficiently in RNase L knockout mouse embryonic fibroblasts (MEFs) than in wild-type cells. This is surprising, as RNase L is known to be an antiviral protein, degrading RNA in response to viral infection. One explanation involves the interaction of alphaviruses with host RNA-binding proteins. Studies performed primarily with the alphavirus Sindbis virus (SINV) have shown the RNA binding protein HuR binds with high affinity to alphavirus RNA through sequence elements in the 3’ untranslated region (UTR), resulting in increased stability of viral RNA. Stability of some host transcripts is also reduced during infection. Tristetraprolin (TTP) is another RNA-binding protein that binds competitively with HuR and promotes RNA degradation. TTP has been found to recruit RNase L to cellular transcripts under mitogen stimulation, resulting in the degradation of these transcripts. We hypothesised that in SFV infected cells, viral RNA binds HuR and sequesters the protein from cellular transcripts. HuR protects viral RNA from being bound by TTP, preventing TTP from recruiting RNase L and degrading the viral RNA. Cellular transcripts with no HuR bound remain vulnerable to TTP binding and RNase L degradation, leading to reduction of cellular transcripts, and therefore reduced translation of cellular proteins. This reduces the competition for translation of viral proteins and therefore results in increased viral replication. Consistent with studies in SINV, we have shown using immunofluorescent microscopy that HuR relocalises from the nucleus to the cytoplasm during SFV infection. Preliminary results of siRNA knockdown experiments also suggest HuR increases SFV replication efficiency. However, we could not conclusively determine if TTP knockdown affected SFV replication. Through transcriptomic analysis of SFV-infected WT and RNase L KO MEFs we found that RNase L was not responsible for the majority of changes in cellular transcript levels or stability during SFV infection. Based on these results, we concluded that our initial hypothesis that RNase L and TTP increases SFV replication efficiency by degrading cellular transcripts is not correct. To find other ways RNase L may benefit alphavirus replication, we investigated the effect of RNase L on stress granules (SGs). Alphaviruses utilise the SG protein G3BP1 to enhance viral replication. To utilise this protein, alphaviruses induce the disassembly of SGs. As RNase L has also been shown to be involved in the disassembly of SGs, we hypothesised that RNase L may also be involved in the disassembly of SGs by alphaviruses. We used immunofluorescent microscopy to investigate whether SGs were present in SFV-infected WT and RNase L KO MEFs. We found that SGs were present in SFV-infected RNase L KO MEFs, but not in the WT. This suggests that RNase L is involved in alphavirus disassembly of SGs.
-
ItemInflammation-dependent differentiation of two distinct regulatory T cell populations in the visceral adipose tissue shapes systemic metabolism( 2022-09)Visceral adipose tissue (VAT) is an endocrine organ critical for energy storage and metabolic homeostasis. It harbours a plethora of immune cells, which play an important role in maintaining tissue homeostasis. A large body of work has shown that type 2 immune cells including T helper (TH2) cells, type 2 innate lymphoid cells (ILC2) and anti-inflammatory macrophages are associated with a healthy VAT and metabolic state. On the other hand, infiltration of inflammatory immune cells, such as CD8+ T cells, pro-inflammatory macrophages, and TH1 cells, result in type 1 inflammation and ultimately lead to insulin resistance and development of metabolic disease. Foxp3+ regulatory T (Treg) cells are critical to restrain VAT inflammation and preserve glucose tolerance. We and others have previously demonstrated that VAT Treg cells are dependent on the adipogenesis transcription factor PPARg and the cytokine IL-33 for their differentiation and maintenance. Further, we have shown that VAT Treg cells display sexual dimorphism on a cellular and transcriptional level. These differences are orchestrated by IL-33 and sex hormones that underpin VAT inflammation and metabolic phenotype. How precisely VAT inflammation and microenvironment shape Treg cell differentiation and function in males and females, however, is still insufficiently known. Here we uncover that the VAT harbours two distinct Treg cell populations, prototypical ST2+ Treg cells, that are enriched in males and depend on IL-33 and PPARg, and a previously uncharacterized population of VAT Treg cells that express the chemokine receptor CXCR3, are enriched in females and depend on the transcription factor T-bet and cytokine IFN-g. We also reveal that the transcription factor GATA3 promoted differentiation of ST2+ VAT Treg cells and together with PPARg and IL-33 repressed the differentiation of CXCR3+ Treg cells. We further show that CXCR3+ VAT Treg cells developed from naive Treg cells in a cytokine IFN-g dependent manner. Finally, we demonstrate that ST2+ Treg cells controlled blood glucose levels, while CXCR3+ Treg cells limited VAT inflammation. Overall, this study establishes the developmental trajectories of two molecularly and functionally distinct Treg cell types in the VAT that act in a sex-specific manner.
-
ItemMedication use of anti-cholesterol drugs and cognitive decline in ageing( 2022-08)Projections estimate 131.5 million will be living with dementia by the year 2050. Alzheimer’s disease is the leading cause of dementia, accounting for about two-thirds of all cases and is a global public health priority. Alzheimer’s disease risk escalates with age and lacks efficacious drugs. Statins are prescribed to lower cholesterol levels and the risk of adverse cardiovascular events. Some epidemiological studies have linked statin use to improved cognitive functioning. Nonetheless, literature in this field is conflicting. Thus, investigations of long-term statin use from midlife have been suggested in recent systematic reviews. To the best of our knowledge, only one study has examined a female-specific cohort, and only few studies have investigated this relationship over a period of at least ten years, and prior to this thesis, no study has examined this relationship in women over a 24-year period. Chapters 1 and 2 examined the current literature regarding statin-cognition relationship. Previous systematic review suggests a mixed and inconclusive relationship between statins and cognitive outcome: however, this thesis provided the first evidence of this relationship extending to the prodromal phase of neuropathological change. A comprehensive systematic review and meta-analysis into statin and cognition found that the significant difference reported in the current statin studies was mainly driven by male statin users. This review highlighted the importance of having long-term statin studies and the urgent need to focus on female statin users. Chapter 4 presented a cross-sectional analysis of the relationship between statin and cognition in participants of the Women’s Healthy Ageing Project. Independent of underlying vascular risk, current statin users, initiation of statin use by women (1-4 years of use) was associated with the greatest deterioration in global cognitive function. This effect is not simply reflective of the lipid levels in the women. Chapters 5 and 6 investigated the longitudinal effect of statin consumption on the cognition of Australian ageing women over time. Participants from the longitudinal Women’s Healthy Ageing Project completed assessments from 1992 to 2016. Statin use by women was associated with greatest decline in episodic memory, global cognitive function and visuospatial ability. Non-statin users were also mostly seen to have a better cognition than statin users across this 24-year period. Type of statins do appear important and the effect of statins on cognition could take up to many years before it is noticeable, highlighting the importance of needing an extensive duration (more than 20 years) of longitudinal studies. This thesis presented the first systematic review and meta-analysis in highlighting the paucity of statin studies with long duration and lack of inclusion of female participants, who are at a much greater risk than their male counterparts. This thesis was the first to examine this relationship in a female only cohort in more than 20 years of follow-up. The results of this thesis, in concert with previous literature, suggest statin has a substantial role in jeopardizing our cognition and the detrimental effects of statins could take many years to be apparent. However; it is clear that the complex connection between statin and brain health requires further research to elucidate the underlying mechanism governing this relationship.
-
ItemNo Preview AvailableUsing Artificial Intelligence to Improve the Diagnosis and Treatment of Cancer( 2022-12)Cancer is a complex and heterogeneous disease driven by the accumulation of mutations at the genetic and epigenetic levels—making it particularly challenging to study and treat. Despite Whole-genome sequencing approaches identifying thousands of variations in cancer cells and their perturbations, fundamental gaps persist in understanding cancer causes and pathogenesis. Towards this, my PhD focused on developing computational approaches by leveraging genomic and experimental data to provide fundamental insights into cancer biology, improve patient diagnosis, and guide therapeutic development. The increased mutational burden in most cancers can make it challenging to identify mutations essential for tumorigenesis (drivers) and those that are just background accumulation (passenger), impacting the success of targeted treatments. To overcome this, I focused on using insights about the mutations at the protein sequence and 3D structure level to understand the genotype-phenotype relationship to tumorigenesis. I have looked at proteins that participate in two DNA repair processes: primarily non homologous end joining (NHEJ) along with eukaryotic homologous recombination (HR), where missense mutations have been linked to many diverse cancers. The molecular consequences of these mutations on protein dynamics, stability, and binding affinities to other interacting partners were evaluated using in silico biophysical tools. This highlighted that cancer-causing mutations were associated with structure destabilization and altered protein conformation and network topology, thus impacting cell signalling and function. Interestingly, my work on NHEJ DNA repair machinery highlighted diverse driving forces for carcinogenesis among core components like Ku70/80 and DNA-PKcs. Cancer-causing mutations in anchor proteins (Ku70/80) impacted crucial protein-protein interactions, while those in catalytic components (DNA-PKcs) were likely to occur in regions undergoing iii purifying selection. This insight led to a consensus predictor for identifying driving mutations in NHEJ. While when assessing the functional consequences of BRCA1 and BRCA2 genes of HR DNA repair at the protein sequence level, this methodology underlined that cancer-causing mutations typically clustered in well-established structural domains. Using this insight, I developed a more accurate predictor for classifying pathogenic mutations in HR repair compared to existing approaches. This broad heterogeneity of cancers complicates potential treatment opportunities. I, therefore, next explored the properties of compounds potentially active against one or various types of cancer, including screens against 74 distinct cancer cell lines originating from 9 tumour types. Overall, the identified active molecules were shown to be enriched in benzene rings, aligning with Lipinski's rule of five, although this might reflect screening library biases. These insights enabled the development of a predictive platform for anticancer activity, thereby optimizing screening libraries with potentially active anticancer molecules. Similarly, I used compounds' structural and molecular properties to accurately predict those compounds with increased teratogenicity early in the drug development process and prioritize drug combinations to augment combinatorial screening libraries, potentially alleviating acquired drug resistance. The outcomes of this doctoral work highlight the potential benefits of using computational approaches in unravelling the underlying mechanisms of carcinogenesis and guiding drug discovery for designing more effective therapies. Ultimately, the predictions generated by these tools would improve our understanding of the genotype-phenotype association, enabling promising patient diagnosis and treatment.
-
ItemThe role of lipids in the formation of beneficial interactions between plant roots and soil microbiota under heat stress( 2022-11)Climate change, which is characterized by the rise of global atmospheric temperatures known as global warming, has serious detrimental effects on crop production because of the direct influence of elevated temperature on plant development. One novel strategy to increase crop productivity while mitigating heat stress is the use of soil microbes, which is slowly gaining popularity because of its low-cost approach, availability, sustainability, and quick turnover. Specific soil microbes can form symbiotic relationships with the roots, whose beneficial effects on plant growth and development, as well as on plant responses to biotic and abiotic stresses, lead to improved plant performance. The plant-microbe interaction is complex and involves below-ground communication, followed by modifications of molecular, biochemical, and morphological processes in the plant. Plant roots display extreme plasticity in adapting to a range of environmental stimuli and are therefore important indicators of plant-level responses to microbial colonization, via changes in architecture and metabolic processes. Lipids, which are essential constituents of the plasma membrane with diverse functions in cellular processes and homeostasis, have been proposed to play significant roles in the rhizosphere. Because heat stresses have a profound effect on membrane stability and lipid composition, rising global temperatures are likely to impact the formation of plant-microbe symbiosis. This study aimed to characterize and quantify the bacteria-induced growth promotion and heat tolerance in plants, and to investigate how plant root lipid profiles are altered under both bacteria and high-temperature conditions. For that, advanced phenotyping and lipidomics technology were employed to monitor plant responses to developmental and environmental changes. By using the high-resolution, high-throughput phenotyping platform GrowScreen-Agar II, an open-top plant-bacteria co-cultivation system was optimized utilizing the model plant Arabidopsis thaliana and the plant-growth-promoting rhizobacteria (PGPR) Paraburkholderia phytofirmans PsJN. This allowed for in-depth, tissue- and time-specific root-and-shoot morphological trait characterization, which elucidated the dynamics of bacterial promotion on plant growth. We have quantified the magnitude of bacterial-induced plant stimulation between ambient and elevated temperatures, confirming the excellent benefit of the PGPR in ameliorating the adverse effects of heat stress. These morphological traits were also associated with the root lipid profile using state-of-the-art lipidomics technology, which revealed specific lipid species and their functions in this tripartite interaction. Knowledge gained from this study, besides being fundamental in the understanding of plant-microbe interactions, can also inform research agenda of future directions for microbial studies as potential agricultural and biotechnological solutions in the endeavor to address global food security under climate change.
-
ItemImproved hidden Markov models for continuous gravitational wave searches( 2022-11)The direct detection of gravitational waves in 2015 has ushered in a new way of making astronomical observations and provided a rich stream of data for making astrophysical inferences. The detections reported by the Advanced Laser Interferometer Gravitational-Wave Observatory (Advanced LIGO) and the Virgo detector during their first three observing runs have so far all been compact binary coalescences, which are short duration signals from the late stages of compact object mergers. There is much left to be discovered, and this thesis advances the state of the art in searches for continuous wave signals: persistent, relatively-weak signals from sources such as neutron stars. The thesis describes two significant improvements to the hidden Markov model (HMM) scheme often used for continuous wave searches, applies the HMM to a search of LIGO Observing Run 2 (O2) data, and describes two ancillary improvements (graphics processing unit optimisation and few-bit digitisation) that improve the performance and memory-efficiency of the implementation. HMMs are used in continuous wave searches to account for spin wandering: small stochastic variations in signal frequency. They work by splitting detector data into short time segments, calculating a detection statistic as a function of frequency at each segment, and then tracking the most likely path for the signal frequency based on a user-specified transition model (an unbiased random walk in this thesis). We introduce a detection statistic called the J-statistic which is sensitive to sources that are part of a binary system. The J-statistic reliably detects signals weaker by a factor of four compared to the Bessel-weighted F-statistic, the previous detection statistic used in HMM searches for binary sources. This improved HMM scheme allows searches for binary sources to be as sensitive as searches for isolated sources. We use the J -statistic HMM pipeline, called "version 2", to search LIGO O2 data for gravitational radiation from the low-mass x-ray binary Scorpius X-1 over a 60-650 Hz frequency band. While no detection is claimed, three candidates survive our follow-up veto procedure. Assuming a non-detection, the search sets a 95 per cent confidence upper limit on strain h_0 of 3.47e-25 at 194.6 Hz when marginalising over the inclination angle of the source. One drawback of the HMM is that each time segment is combined incoherently: version 2 of the HMM does not enforce a consistent signal phase in the transition between blocks. We introduce version 3 of the HMM, which does track inter-block phase. The result is a detection pipeline, applicable to either isolated or binary sources, that is a factor of ~1.5 more sensitive than version 2, and closes much of the gap between the HMM and a fully-coherent search while retaining the computational efficiency of earlier HMM versions. We describe an implementation of the J -statistic and HMM on graphics processing units (GPUs), which provides an order-of-magnitude improvement in processing speed and was essential for covering the wide parameter range used in the O2 Scorpius X-1 search. Running that search using the GPU implementation of the pipeline required approx < 3e5 GPU-hours. We further describe the first application of few-bit digitisation techniques to continuous gravitational wave search methods, finding a decrease in sensitivity of only 6 per cent (two-bit digitisation) or 25 per cent (one-bit) in return for a factor of 32 or 64, respectively, reduction in memory use.
-
ItemComparison of measured and perceived fundamental characteristics to identify strategies for increasing the rate of daily walking in suburban areas( 2020-07)Future cities will increasingly face health, socio-economic and environmental problems, including disease, social isolation, economic breakdown, excessive carbon dioxide emissions, climate change, and fossil fuel depletion. The planning and design of neighbourhoods which provide high levels of pedestrian accessibility to daily needs destinations such as schools, grocery shops, greenspaces and public transport could contribute to solutions to these problems by the reduction of car-based travel. Future cities need to be walkable based on solutions that can be achieved through better planning and design which takes into consideration accessibility as well as Key Urban Place Characteristics (KUPCs). The author considers walkability to be formed by two factors: the first, accessibility, is the distance to daily needs destinations, and the second is KUPCs, the safety and security, comfort, and attractiveness of the walk to those daily needs’ destinations. Although many suburban neighbourhoods in Melbourne have good access to daily needs, people who live in these areas often choose to drive to their destinations rather than walk. This may be due to negative perceptions of the place and the lack of fundamental place characteristics. The aim of this research is to identify strategies to increase rates of daily walking based on an understanding of the relationship between urban place characteristics and accessibility in suburban neighbourhoods. Therefore, the author has chosen four case studies; two international best practice case studies to validate a theoretical framework obtained from the best practice literature, and an in-depth examination of two local case studies in Melbourne using the validated theoretical framework to assess the scale of walkability in the most accessible areas in selected suburban samples. Both quantitative and qualitative methods are used in this study, in keeping with a sequential explanatory design mixed-method approach. Data collection was conducted using mapping, urban informatics, desktop analysis, field observations of KUPCs, and face-to-face interviews with residents. The analysis of walking-related values using key research studies provided opportunities to reveal the most important characteristics needed for walking to daily needs in the case studies. These results were used to identify strategies for increasing the rate of daily walking in suburban areas.
-
ItemHere, you can live well: Pollution, rural livelihood and the hardness of place on Lake Titicaca, Bolivia( 2022-11)This thesis gives an ethnographic account of how Quehuaya, an Aymara community on Lake Titicaca, Bolivia, is navigating a future circumscribed by water pollution, climate change and the policies of the Movement toward Socialism (MAS) government. As rural livelihoods such as fishing and agriculture become increasingly unviable, a collective life lived in dialogue with the landscape is coming under threat. In response, community members make use of emerging opportunities presented by the MAS indigenist-developmentalist program, the burgeoning urban economy of the nearby city of El Alto, and ongoing opportunities for migration. I develop an account of the hardness of place itself – its solidity in the face of flux – to foreground the dynamics underlying its ongoing but shifting role in this turbulent and threatening context. To unravel the dynamics underlying the hardness of Quehuaya as a place, I demonstrate how the community is reproduced through an Andean collectivism built on practices of livelihood, landscape ritual and syndical political organisation. I analyse how these express Andean ontologies of place, as enmeshed with collectivity and the non-human. Central to my argument is a dialogic theory of agency, which accounts for both individual and collective forms of agency as emergent from a prior intersubjectivity. The hardness of place in Quehuaya rests on the dialogue between the collective will and authorities responsible for establishing relations with the exterior worlds of both landscape and the institutional sphere. This is key to reproducing a cosmology of circulation that constitutes the community in place. This attention to dynamics enables an analysis of ontologies of place that avoids an excessive constructivism that would elide their determining power, without collapsing into essentialism. I demonstrate how in Quehuaya, the cosmology of circulation and the modes of personhood associated with it are threatened as its constitutive relations are disrupted. This is affecting the role of place as an anchor for collective identity and the political possibilities of response to the pollution crisis. I further demonstrate how community members strive to re-establish the stability of place through innovation in livelihood and engagements with state and development actors. These efforts promise to use the material, cultural and relational resources of place to renew the circulatory flows on which it depends, and thereby re-establish the authority of landscape. However, this pursuit of increased articulation with a wider world through novel forms of engagement with the global economy – such as tourism – and the contradictions of the MAS state exacerbates fundamental tensions between individual and collective forms of agency. While the scale of changes threatens to overwhelm the community’s ability to integrate them, I argue that the techniques of Andean collectivism are fundamentally oriented towards the maintenance and steering of collective trajectories in an inherently unpredictable and dangerous world, and a recognition of the unavoidable limits of human agency. This thesis thus offers a contribution to the theorisation of collective life in the context of a shared world becoming increasingly uncertain for all of us.
-
ItemSafety of Bacille Calmette-Guérin vaccination and revaccination( 2022-12)Bacille Calmette-Guerin (BCG) vaccine, derived from live-attenuated Mycobacterium bovis, is commonly given as a single dose in infancy to protect against tuberculosis (TB) in high TB-prevalence settings. There is growing interest in BCG revaccination for the protection of adolescents and adults against TB. Increasing recognition of potential novel applications for BCG to protect against diseases other than TB also mean that BCG vaccination (and revaccination) may become increasingly used in broader age groups and settings. For these reasons, a more comprehensive and detailed understanding of the safety of BCG vaccination and revaccination, particularly in adults, is necessary to help inform public health policy. My PhD research aimed to evaluate the incidence and predictors of reactions (normal, accelerated and adverse) to BCG vaccination, the impact of revaccination on BCG reactions, and the clinical management of adverse reactions to the vaccine. These aims were investigated using active safety surveillance of BCG vaccination reactions within an international randomised controlled trial of nearly 7000 adult participants – the BRACE Trial (BCG vaccination to reduce the impact of COVID-19 in healthcare workers), as well as through two systematic reviews and a meta-analysis of BCG vaccination safety in children. My thesis comprises three sections characterising reactions following BCG vaccination and revaccination: (i) the normal reaction; (ii) accelerated reactions; and (iii) adverse events. The first section reports a cohort study to assess the prevalence, factors influencing formation and vaccinee perception of BCG scarring (normal BCG reaction) following vaccination and revaccination in adults. The second section includes a systematic review and meta-analysis to investigate the clinical significance of an accelerated BCG reaction in children, reporting an association with prior mycobacterial exposure. A cohort study is then presented that evaluated the incidence and clinical implications of an accelerated BCG reaction in asymptomatic adults in low and high TB-prevalence settings. The third section includes a systematic review of the management strategies for BCG-associated lymphadenitis and injection site abscess in children. This is followed by a cohort study to assess the incidence and risk factors (host immune- and vaccination-related) for BCG-associated lymphadenitis and injection site abscess in adults. An additional cohort study in adults assesses the safety of co-administration of BCG with the influenza vaccine. The overall incidence of local adverse events and serious adverse events in the BRACE trial is then described, as well as the impact of previous BCG vaccination on local injection site reactions. Overall, BCG revaccination in adults was associated with increased frequency of normal (scar), accelerated and local adverse reactions (injection site abscess and lymphadenitis), compared to receiving BCG for the first time. Younger age was also associated with increased frequency of normal and local adverse reactions. Similarly, female sex was associated with an increased frequency of normal reactions and lymphadenitis following BCG vaccination, as well as increased frequency of accelerated BCG reactions. Latent TB infection was found to predispose to an accelerated BCG reaction, but was not associated with injection site abscess. Nonetheless, regardless of prior BCG vaccination status, age or sex, the majority of reactions were mild in nature, localised to the injection site and resolved without intervention. In summary, the studies in my thesis indicate that BCG vaccination and revaccination have an acceptable safety profile in children and adults.
-
ItemThe Language of Archaeological Investigations( 2022-08)The thesis explores whether methods based upon analogical reasoning can be used to interpret culture if there are difficulties of translating other culture’s beliefs. The kind of cultural interpretation that I will discuss is that which pertains to social, artistic and religious activities. The thesis also explores the differences between quantitative and qualitative forms of reasoning, as well as inductive an deductive approaches, and how these are used in certain forms of archaeological interpretation. It is shown that scientific analyses of culture can make errors of translation, and it is also shown that humanistic and qualitative analyses of culture make many errors of reasoning that may be usually put forth against scientistic analyses of culture. How much biology and culture influence statistical trends is also discussed, and it is argued that trends may give support to certain forms of analogical reasoning that an archaeologist might use for the interpretation of culture. I also critique the idea of biological universals as being meaningful for cultural analysis. It is also argued that cognitive and biological factors exist below the level of cultural and religious activities; hence, a biological basis for statistical trends might not give much content to certain forms of comparative cross-cultural analysis. Thus, one might defend a qualitative approach to interpretation, but I argue that qualitative approaches make errors that can be paradoxically regarded as scientistic. The relevance of philosophical and linguistic theories by Kant, Kripke and Carnap is defended for archaeological research to explore interpretative errors in both quantitative and qualitative reasoning. The thesis argues against the dualism between the qualitative and quantitative, and attempts to argue for a pluralist methodology where positivism and relativism may be unified.