VictorJuiz/thesis huggingface dataset:
The effects of lysosomal Ca2+ release on membrane depolarisation and synaptic plasticity in hippocampus

Intracellular Ca2+ signalling is essential for the control of almost every physiological process, from muscular contraction to synaptic transmission. Intracellular Ca2+ signals can be generated from both extracellular or intracellular Ca2+ stores. Nicotinic acid adenine dinucleotide phosphate (NAADP) is a ubiquitous and important Ca2+ mobilising second messenger. NAADP signalling causes Ca2+ release from intracellular acidic Ca2+ stores. The functional roles of NAADP signalling and acidic store Ca2+ release in the central nervous system are relatively unknown Brailoiu et al. (2009b) showed that NAADP signalling enhances membrane excitability in neurons of the medulla, Padamsey and Emptage (2011) (Unpublished) find similar effects in pyramidal neurons of the hippocampus. I used pharmacological manipulations in combination with electrophysiological techniques and dendritic Ca2+ imaging to explore the effect of NAADP/acidic store signalling on membrane excitability and synaptic plasticity in pyramidal neurons of the hippocampus. I began by using a membrane permeable form of NAADP (NAADP-AM) to show NAADP/acidic store Ca2+ signalling caused membrane depolarisation. I also showed, with intracellular dialysis of Ca2+ mobilising second messengers, NAADP is unique in its ability to directly cause membrane depolarisation. I then identified glutamate, acting via metabotropic glutamate receptor 1 (mGluR1), as an endogenous stimulus that causes NAADP-mediated Ca2+ release and depolarisation. I next elucidated the signalling pathway responsible for mGluR1/NAADP-mediated depolarisation and showed the requirement of acidic store Ca2+ release, and subsequent amplification of this Ca2+ via ryanodine receptors by Ca2+-induced Ca2+ release. The resulting Ca2+ signal caused inhibition of small conductance K+ channels (SK channels) and membrane depolarisation. SK channels are described to facilitate the induction of plasticity in hippocampal synapses by modulation of GluN Ca2+ entry (Ngo-Anh et al., 2005). Finally, I show that the induction of mGluR1-dependent long-term potentiation requires inhibition of the SK channels via NAADP/acidic store Ca2+ signalling. Group 1 mGluRs are implicated in the pathogenesis of neurodevelopmental disorders such as fragile X syndrome. My findings may identify new targets for the treatment of such diseases.

Advisor: Emptage, N
Galione, A
Synthesis of eleutherobin-like potential microtubule stabilising agents

This thesis describes synthetic studies towards the tricyclic terpene framework of the cytotoxic natural product eleutherobin, and the investigation of biocatalytic methodology towards late stage functionalisation of the structure.
Chapter 1 provides an introduction to the biomedical significance of the natural product and to the various synthetic studies reported to date.
Chapter 2 explores intramolecular Diels–Alder approaches to the construction of the nine- and six- membered rings present in the natural product.
Chapter 3 describes alternative approaches to the eleutherobin core structure, leading to a formal synthesis of the natural product. The synthetic sequence developed is applied to the preparation of a small library of furanoid analogues of eleutherobin.
Chapter 4 details the development of methodology for the one-pot preparation of (E)-4-methylhexa-3,5-dien-1-ol, and its use in an intermolecular Diels–Alder / lactonisation sequence to achieve enantioselective preparation of an important lactone building block.
Chapter 5 describes studies on the mP450-mediated oxidation of various eleuthoside structures obtained.
Finally, Chapter 6 details the construction of an electrochemical flow cell, and its use for the anodic oxidation of furfuryl alcohol derivatives.

Keywords: Diels-Alder reactions
biocatalysis
cytochrome P450
natural products
eleutherobin
Advisor: Robertson, J
Characterisation of a New p97 Adaptor in Genome Stability

Cells are subjected to constant genotoxic stress arising from both endogenous and exogenous sources which can drive the development of a wide range of diseases, especially cancers. Therefore, repair of these lesions is essential to maintain genomic stability and health. The DNA damage response is a key aspect of this process and requires the temporal and spatial regulation of many different factors to orchestrate the repair process. This requires the action of the AAA ATPase p97 which acts as a molecular segregase in order to facilitate the turnover of proteins on chromatin. This is also a crucial process to prevent the collision of DNA replication and transcription machinery with DNA bound proteins and DNA structures. These processes require the action of p97 cofactors which direct p97 to specific substrates and biological functions. The role of p97 and its cofactors in the DNA damage response is beginning to emerge, however there is still much to be investigated. Therefore, this thesis focuses on the characterisation of a new p97 adaptor protein discovered during a Mass Spectrometry analysis of the p97 interactome in response to ionising radiation. This adaptor protein, which has been named Ionising Radiation Enhanced VCP Interacting Protein 1, or IREVIP1, is responsible for maintaining genome stability even in unchallenged conditions. IREVIP1 was found to interact directly with p97 via a SHP domain located in the C-terminus of IREVIP1, as well as with Topoisomerases, and is responsible for bridging their interaction. IREVIP1 was observed as being part of the replication fork, and was required to prevent the accumulation of Topoisomerase cleavage complexes. Thus, IREVIP1 could be required to prevent genomic instability arising from collisions with Topoisomerase cleavage complexes and DNA structures arising from excessive DNA torsion. Therefore, this thesis begins to characterise the novel adaptor IREVIP1 and its functions within the cell.

Advisor: Ramadan, K
The rebel governance of the SPLM/A and UNITA: a comparative study on parallel states in Angola and South Sudan

This is a study of rebel political orders and the degree of governance rebels can install in their liberated areas. It studies the ways in which force came to be transformed into authority under the rule of two military organisations fighting asymmetrical wars in highly divided societies. Wartime rebel states are by nature an exercise in control and power, in projecting authority and symbolism, in managing contradictions and shortcomings, but are also deeply revealing of the characteristics of rebel movements, their motivations, survival strategies and organisational capacity. This thesis on the rebel governance of União Nacional para a Independência Total de Angola (UNITA) and the Sudan People’s Liberation Movement/Army (SPLM/A) is a study on how two very different reform rebel movements, fighting two of Africa’s deadliest and recurrent civil wars, devised and designed institutions to govern civilian populations in the stable liberated areas of Jamba in Angola and Yambio in South Sudan. Existing governing strategies were reformed after both faced critical junctures that exposed the fragilities of their organisations, the insufficient coordination of structures and leadership, and the need to reformulate an ideology to rally widespread support across constituencies.
Their parallel states emerged as a key pillar to survive and win their second liberations. The Free Lands of Angola embodied UNITA’s centralised and totalitarian state project. The New Sudan embodied the SPLM/A’s decentralized approach to governance and its pragmatism of local alliances. This comparison is structured around four internal agentic elements of these two movements: their leadership, ideology/political program, organisation and approach to civilians. This allows for mutually reinforcing explanations of what informed their parallel states and contextualizes strategies and motivations by exposing a ‘rebel-system’ as a theory of operation accounting for change and highlighting elements that powered the movements and their liberation struggles.

Advisor: De Oliveira, RS
Assessing the influence of anthropogenic disturbance on sympatric felids on Borneo with special reference to the Sunda clouded leopard

For decades, Borneo's once extensive and pristine forests have been increasingly exposed to a suite of anthropogenic disturbance and deforestation processes as a result of selective and illegal logging, hunting, droughts, fires and the conversion to plantations, chiefly oil palm. Such disturbance is likely impacting the Sunda clouded leopard, Neofelis diardi, and other threatened, sympatric Bornean felids, yet few studies have attempted to address these issues. In this thesis, I used data from intensive camera trap surveys throughout Sabah, Malaysian Borneo and high-resolution GPS data from tagged Sunda clouded leopards to examine the influence of forest disturbance on the abundance, distribution, movements and population connectivity of Sunda clouded leopards and other sympatric felids on Borneo, and to provide some of the first data regarding the ecological interactions and patterns of coexistence among this felid assemblage. I showed that Sunda clouded leopard movement was facilitated by forest cover with high canopy closure, and highly resisted by oil palm plantations with low canopy closure. Models of population connectivity across Sabah identified a number of isolated populations of these felids, which may be particularly threatened with extinction. Analysis of camera trap detection data revealed that the Bornean felids exhibit evidence of resource segregation along the temporal, spatial and prey niche axes, and showed that Sunda clouded leopards, bay cats, Catopuma badia, and marbled cats, Pardofelis marmorata exhibited broad scale avoidance of disturbed habitats but varied in their selection of optimal foraging habitat at fine scales. Conversely, leopard cats, Prionailurus bengalensis, were associated with forest disturbance and likely benefit from such changes. I developed some of the first estimates of population density for Sunda clouded leopards and the first such data for marbled cats. The results are discussed in the context of the conservation of these felids on Borneo.

Keywords: Borneo
population density
niche separation
Sunda clouded leopard
population conectivity
Advisor: Macdonald, D
Hunter, L
Mechanical and geometric cues guiding early mammalian tissue development

Mammalian development is one of the most complex biological processes, that is responsible for converting a single cell into a whole organism. Al- though, mechanical forces are expected to play profound roles during de- velopment, proving the role of mechanical and geometric cues has been difficult due to the lack of suitable experimental techniques. The thesis investigates the hypothesis, that mechanical and geometric cues are driv- ing the first two cell fate decision events. In order to test them and create a robust experimental framework, the first three chapters are dedicated to developing methodology based on three dimensional patterned hydrogels. The hydrogels were mechanically and biochemically characterised in high detail and then used as three dimensional moulds to shape developing tis- sues. This technique also made it possible to calculate mechanical forces, which could be estimated from hydrogel deformation and known elastic properties. Finally, to characterise the biological outcomes of mechani- cal tissue deformation a heuristic confocal image analysis technique has been developed and used to investigate developing mammalian tissues. Using the techniques it was possible to demonstrate, that the first cell fate decision is controlled by embryo geometry and the molecular mecha- nism involved a complex combination of Hippo pathway signalling and a sequence of cell polarisation. Similarly, the second cell fate decision was also found to be driven by tissue geometry and Hippo pathway signalling, although the precise biochemical pathway was less clear.

Advisor: Srinivas, S
Vollrath, F
Royer, C
‘[I am] unable to refuse the call of these pages to be scribbled in’:  The Function of First World War Life-Writing

Drawing on a diverse collection of both published and unpublished First World War diaries and letters, this thesis investigates the role of composition in war, examining the ways in which the act of writing itself—imposing narrative order on chaotic experience—functions in creating, securing, and repairing one's multiple identities in war. Indeed, through narration, the individual can connect to, challenge, or reconfigure, the war's prescribed social scripts—of soldier, nurse, spouse, parent, and/or patriotic citizen. This process or writing, and thereby re-asserting, one's identity was a fundamental component of men and women’s emotional survival. In the midst of the First World War's chaos, life-writing held heightened significance on both home and battlefront. The diary and letter were appropriate generic vehicles through which men and women could express and negotiate the new facets and fragments of self; they were also sites where different social scripts could be tried and rehearsed, and venues for the navigation of war's trauma, suffering, and grief. Through the act of writing, the individual imposes some level of control over this otherwise chaotic experience. The 'I' on the page—whatever the length or descriptive quality of the words that surround it—is an assertion of the individual in a culture of sweeping propagandist claims, mass movement, and mass death. By putting pen to paper, the newly enlisted man could attempt to navigate the seemingly rapid transition from ordinary civilian to heroic soldier; the home front mother could confess fears and frustrations on the diary page, in turn mitigating grief and navigating the sense of self—as mother, as wife, as patriotic citizen—in the face of loss; from his trench, the frontline combatant could find distraction and escape through writing a letter home. The civilian man, in turn, could seek refuge in the diary’s pages—his search to secure and validate alternate forms of ‘manliness’ often being particularly fraught.

Keywords: First World War
Diary
British Literature
Cognitive psychology
Identity
Trauma
Medical Humanities
Letter
Advisor: Marcus, L
International courts and legal innovation: the politics and practices of interpretation in international criminal law

In international criminal law (ICL), legal meaning has been developed substantially through the judgments of international courts. Compared to some of their prosecutorial decisions, however, the way in which international judges have interpreted legal provisions has remained relatively uncontested. This study uses practice theory as a particularly fruitful lens through which to study the politics of legal interpretation. It analyses the conditions under which the creation of a comparatively uncontested judicial space became possible as an interplay between political commitments and the professional assumptions of ICL experts. The study argues that international criminal courts – unlike hybrid courts – have been accorded a particularly high degree of interpretive authority through what will be called the ‘practice of privileged precedent.’ It traces how this interpretive practice has been shared across institutional settings within a broader interpretive community, including by government officials and civil society representatives. Through this research, this thesis emphasises the relevance of legal interpretation for IR’s understanding of international law and international courts. Drawing on legal theory, it also addresses one of the key challenges of IR’s practice turn: its capacity to account for the creative potential of international practices.
Methodologically, the thesis combines qualitative and quantitative forms of content analysis, elite interviews, and legal interpretive methods. It is based on an examination of over 100 judgments of international and hybrid criminal courts interpreting the crime of genocide and the law of war crimes, including judicial decisions delivered by the International Criminal Court (ICC), the International Criminal Tribunal for the former Yugoslavia (ICTY), the International Criminal Tribunal for Rwanda (ICTR), and the Special Court for Sierra Leone (SCSL). This analysis is supplemented by 28 elite interviews with judges and legal experts at international criminal courts, staff at civil society organisations, and government officials working for the British and German foreign offices.

Keywords: International Criminal Court
international law
international criminal law
legal interpretation
Advisor: Hurrell, A
Investigating the role of alternative polyadenylation in neuronal differentiation and neurodegeneration

Over 70% of human genes can undergo alternative polyadenylation (APA), whereby they utilise different polyadenylation (poly(A)) sites found in the 3’UTR (3’UTR-APA) or in the upstream coding region of the gene (upstream-APA). The 3’UTR harbours regulatory cis-elements which can mediate the stability, translatability and localisation of the mRNA. Therefore, modulating 3’UTR length through APA can affect downstream gene expression. The UTR landscape can be modified through altered poly(A) site choice during transcription, or in a post-transcriptional manner, via interaction with miRNAs or RNA binding proteins. Global shifts in UTR length have been identified in different tissues and cellular states. Using a combination of molecular biology and bioinformatics approaches, this thesis assesses changes in APA profiles regulated by transcriptional and post-transcriptional APA during neuronal differentiation, in neurodegeneration and in cellular stress. The BE(2)-M17 neuroblastoma cell line was used to model neuronal differentiation. Here, the trend to UTR lengthening in differentiation was attributed primarily to post-transcriptional not transcriptional APA regulation. APA in neurodegeneration was assessed using an in vitro model and publicly available RNA-seq datasets were bioinformatically interrogated to assess UTR length changes in Alzheimer’s Disease, Parkinson’s Disease and Amyotrophic Lateral Sclerosis. While global APA changes were not observed, genes associated with pathophysiological pathways were identified, highlighting the important role of APA mediated gene expression in neurodegenerative diseases. Exposure to cold shock and hypoxia showed differential APA regulation. Interestingly, moderate hypothermia caused a trend to 3’UTR lengthening, even in combination with other stress inducers. These UTR-lengthened genes exhibited binding sites for proteins that associate in stress granules. Therefore, APA regulation may contribute to the aggregation of mRNAs in stress granules during stress conditions. In conclusion, this thesis identifies an unprecedented role of post-transcriptional regulation of the UTR landscape, and identifies physiologically relevant genes regulated by APA during the changing cellular environment.

Advisor: Furger, A
Schools and student obesity: research into school-level environmental associations and student weight-related factors

Background: This thesis investigated the role that primary schools play in promoting healthy eating and physical activity (PA) amongst students. The socio-ecological model (SEM) to health provided the theoretical framework for understanding the different levels of influence on childhood obesity. A systematic review of the evidence was published that looked at the relationship between the school setting and rates of student overweight and obesity (O&O;). Its primary aim was to examine if there was a significant association between student Body Mass Index z-scores (zBMI) and the number of school environmental actions in place to promote healthy eating and PA amongst students.
Methods: As part of a larger-scale investigation into childhood obesity led by the World Health Organization (WHO) Collaborating Centre for Childhood Obesity in Victoria, Australia, student- and school-level data were collected using objective measures of student weight outcomes and self-report behavioural questionnaires (providing individual-level data), along with the Be Active Eat Well (BAEW) school environmental questionnaire (providing school-level data). Descriptive and regression analyses were completed to investigate statistical associations between student zBMI and results from the BAEW questionnaire, including once adjusted intermediary factors and clustering.
Results: From a sample of 715 Year 4 and 6 students across 34 primary schools, males reported a significantly higher prevalence of O&O; than females (34.3% and 28.7%, respectively) and further analyses were split by gender. Indigenous Australian students reported significantly higher rates of zBMI than non-Indigenous Australians (p-value = 0.001), but with only a small sample size (n = 23). A range of significant associations were found between individual-level factors. Fully adjusted multivariate regression models reported a significant association between student zBMI and the amount that schools did to promote healthy eating amongst female students (p-value = 0.007).
Conclusion: The number of school-level actions in place to promote healthy eating was significantly associated with student zBMI in girls. This thesis was supportive of the hypothesis that schools play an important role in the prevention of childhood O&O.; It makes a unique contribution to the evidence-base in terms of the methodology behind the study of school effects on student weight outcomes. It promotes the adoption of a socio-ecological approach to childhood obesity prevention, focused across all levels of society, and provides direction for future research and policy and legislation aimed at preventing childhood obesity in Australia and elsewhere.

Advisor: Plugge, E
Foster, C
Allender, S