VictorJuiz/thesis huggingface dataset:
Characterising root attachment in Rhizobium-legume symbioses

In Rhizobium-legume symbioses the earliest stage of physical contact between bacteria and the plant root is primary root attachment. This is crucial for nitrogen-fixing symbiosis development and underpins many plant growth-promoting relationships. Rhizobia use a variety of factors for primary attachment including pH-dependent adhesins (such as glucomannan and the hypothesised rhicadhesin), surface proteins and extracellular polymeric substances. However, primary attachment remains an understudied area of symbiosis development.
In this work I use a range of techniques including luminescence-based attachment assays, mariner insertion sequencing (INSeq) and real-time imaging to investigate the factors governing primary attachment to plant roots with the model organism Rhizobium leguminosarum biovar viciae 3841. These techniques demonstrate that bacterial cell surface and extracellular factors are crucial and show extensive pH-condition and plant host specificity. Exopolysaccharide, lipopolysaccharide and peptidoglycan all show different profiles of modification in attachment to pea roots at different pHs and attachment to barley and soybean roots. The glycolytic enzyme TpiA is likely to be surface localized and is an attachment factor required under all conditions. Further, outer membrane protein and Flp/Tad pilus usage in attachment to soybean and barley roots shows that Rlv3841 can use primary attachment mechanisms demonstrated in other bacterial species. Another novel insight is that a filamentous hemagglutinin adhesin factor is also a previously unknown primary attachment factor. Proteomics, attachment assays, INSeq and confocal imaging were used to investigate rhicadhesin, demonstrating that there are multiple attachment factors matching the criteria for this protein. As glucomannan-independent root hair attachment is shown to be both polar and non-polar, these factors are likely distributed across the cell surface. Results from INSeq showed that control of cyclic-di-GMP levels is another important parameter in root attachment. It seems likely that the regulator RL4145 (required for attachment to all plants tested) functions via repression of a cyclic-di-GMP degrading factor to promote attachment. This work also builds on root-microbe interaction imaging technologies by developing a system suitable for Rhizobium and legume plants. Results reinforced the idea that the root elongation zone is a crucial region for early stage interactions, and that bacterial cell motility is important for this. Overall, this work significantly enhances our understanding of primary attachment mechanisms in Rhizobium-legume symbioses, demonstrating a previously unknown mechanistic complexity.

Advisor: Poole, P
The application of new sampling methods to previously inaccessible tropical forest areas with particular reference to Papua — New Guinea

This paper establishes the need to evaluate the forest resource of developing countries as a preliminary to forest industry development. ‘The purposes of forest resource inventory are defined as supplying information for -
(i) long-term policy planning
(ii) the evaluation of forest areas for exploitation investment
(iii) direction of more detailed management investigation.
The requirements of a single inventory are to provide data on the physical, biological and economic aspects of a forest area. The biological and economic data requirements are of principal concern in this paper.
The application of forest resource inventory in Papua - New Guinea is reviewed in the light of existing and potential forestry development. The history of attempts at assessment of the forest resource of the territory has revealed that at no time have entirely objective methods been employed. It is contended that subjective methods have no place in extensive forest inventory.
[Summary continued in thesis]
A logical theranostic CRISPR/Cas system and novel carriers for its delivery

Nucleic acid-based therapies hold the promise to treat many diseases in a way that was not previously possible: at the genetic level. Unfortunately, these therapies are limited by a lack of efficient delivery systems. It is challenging to synthesise new delivery systems that can effciently reach specific tissues. This is because new delivery systems need to overcome many sophisticated biological barriers, from avoiding the immune system to escaping the endosomal pathway. Better delivery systems would make nucleic acid therapies a reality.
I tackle this fundamental issue by developing two novel nucleic acid delivery systems: the Polymeric Spherical Nucleic Acids (PSNAs) and the Cell-Derived Vesicles (CDVs). PSNAs are PMPC25-PDPA75 polymersomes decorated with intra- and extravesicular coronas of DNA oligos, which have a great potential as siRNA delivery systems. PSNAs have been designed to overcome the endosomal barrier, through an osmotic shock caused by their pH-dependent disassembly. Because of these characteristics, PSNAs are able to deliver therapeutic siRNA to an Amyotrophic Lateral Sclerosis (ALS) in vitro model. CDVs are bio-inspired delivery systems produced from purified cellular plasma membrane, which confer on them a complex biological identity through their natural lipids and membrane proteins. These vesicles are readily engineered, as plasma membrane from different cell types can be isolated, or cells can be transfected/transduced to express heterologous proteins of interest. This versatility is enhanced by their ability to encapsulate small nucleic acids, such as DNA oligos or CRISPR/Cas9 sgRNA, and functionally deliver them. CDVs are promising delivery systems that may be applied to different diseases.
While delivery is a paramount issue, there is always unspecific in vivo accumulation, as seen by the typical retention of nanoparticles in the liver. For the CRISPR/Cas9 gene editing system, this is dangerous. Unspecific delivery of CRISPR/Cas9 components can result in off-target mutations. To address this problem, I have developed a theranostic CRISPR/Cas system that can perform logic computations with endogenous cell signals, in order to determine if it is in the right environment.

Keywords: Nanomedicine
gene therapy
nucleic acid delivery
CRISPR
Advisor: Turberfield, A
Invasive Caribbean lionfish: ecological impacts, behavioural interactions and habitat use

Lionfish (Pterois volitans and P. miles) have become invasive across the western Atlantic and are considered one of the most heavily impacting invasive marine vertebrates. Most lionfish research focuses on consumptive effects in small-scale patch reef studies, with little research on their behaviour, non-consumptive effects or regional impacts. Using binary choice laboratory experiments, I found that lionfish were not attracted to conspecific cues. Instead, habitat preference likely drives aggregation formation, as in situ observations revealed that lionfish avoid fine-scale complexity but are attracted to broad-scale complexity, such as caves and overhangs. Shelter use by lionfish may impact native shelter-using species, such as commercially important spiny lobsters and ecologically important long-spined sea urchins. I found that lionfish did not affect shelter use by either native species in laboratory experiments, indicating that negative impacts of lionfish from competition for shelter may not be as widespread as feared. Interestingly, lionfish reduced their shelter use in the presence of the native species. I also investigated herbivorous fish grazing as a potential non-consumptive effect of lionfish. By comparing the same small areas of reef with and without lionfish, I found that responses to lionfish varied even within a small reef system, indicating that lionfish presence is not the only driver of the observed changes. The highly variable results of small-scale studies like these highlight the urgent need for regional-scale studies to determine the true extent of lionfish impacts in their invaded range. Prior to this thesis, no research had been conducted into the impacts of lionfish on native fish communities that simultaneously considered sites with different invasion timelines across the western Atlantic. I took a novel approach to understanding large-scale impacts using temporally offset additive mixed models centred on year of first invasion, combining 11,000 transects from eight countries with 14 contextual variables known to affect reef fish communities. I found clear shifts in native fish communities between pre-invasion and two or more years post-invasion, indicating that lionfish invasion rapidly results in a stable change in native fish communities. I found pre-invasion increases in native fish abundance, species richness and diversity that continued in the initial years of the invasion, however, I detected simultaneous declines in all metrics at five years post lionfish invasion. This thesis provides new insights into invasive lionfish behaviour and non-consumptive effects and provides the first suggestion that lionfish exert region-wide impacts by using a novel approach for studying the large-scale impacts of invasive species.

Keywords: Lionfish
Non-consumptive effects
Habitat association
Inter-specific competition
Pterois
Invasive species
Advisor: Exton, D
Lewis, O
Curved spaces admiting solutions to twistor equations

This thesis comprises three sections. In the first, real space-times admitting a solution to the two-index twistor (Killing spinor) equation are constructed and the separability properties of solutions to zero rest-mass field equations within these space-times are derived. In addition conditions for differential relations between components of opposite helicity are derived.
In the second section class of half algebraically-special spaces is investigated, a class which may be characterised as those admitting a certain partial two-index twistor (Killing spinor). A formalism based on their structure as a two-dimensional family of flat null two-planes is developed and used to provide an explicit integration of the curvature equations, to discuss Hertz-type potentials for zero rest-mass fields and to examine a class of Einstein-Maxwell spaces and their perturbations.
In the third section we examine the relation between the space of solutions to the twistor equation restricted to a general space--like two-surface of spherical topology (two-surface twistor space) and its dual. This is then used to discuss the nature of the local embedding of the two-surface in a space conformally related to complex Minkowski space.

Keywords: twistor equations
Twistor theory
general relativity
twistor
curved spaces
relativity
Advisor: Penrose, R
The Greek hero Perseus : myths of maturation

Owing to a certain fascination with the Gorgon and its origins, past scholarship has given less consideration to Perseus as a heroic figure in his own right than might be expected. He is generally thought of as colourless in comparison with heroes such as Heracles, Theseus and Jason. As a body, his myths have in any case received little attention in the last thirty years, and the thesis attempts to redress the balance, to ‘parse’ Perseus by ‘construing’ his myths. He is indispensable to all the myths. The initiatory schema, in terms both of a general rite of passage, and more specifically of ‘ephebic’ motifs, is central, and is established in the introductory chapter (I). The movement of the hero from οικος to πολις, is coextensive with his maturation. The remaining chapters (II-V), on Acrisius, the Gorgon, Andromeda and Dionysus, follow through the process of Perseus’ maturation, from his anomalous birth, exposure, his youthful exploits, acquisition of a wife, to his return to and defence of the πολις, Argos, from Dionysus and his θιασος. He returns to Argos with divine sanction despite all mortal attempts to prevent him: the preservation of the οικος, and by extension the πολις, is key to the characterization of Perseus. His myths are a particularly potent example of the tendency, and imperative for, Greek values of civilization, as represented by the οικος and πολις, to be perpetuated. In this sense, Perseus is a ‘political’ hero. An appendix on the fragmentary Perseus dramas performed in antiquity confirms his popularity throughout the whole of the fifth century and beyond, and shows that, contrary to what the relatively skeletal sources might suggest, he was not simply a cipher, but a fully characterized figure in the Greek imagination.

Keywords: myths
hero
Greek heroes
Greek hero
heroes
Perseus
Advisor: Bowie, A
Influence of inherited genetic variants on risk, biology and prognosis of common cancers

Cancer is a complex disease affected by both inherited risk variants and somatic alterations. Recent studies showed that inherited genetic variants and somatic driver mutations converge in cancer hallmark pathways, and that inherited genetic variants were associated with specific somatic driver mutations in tumours. However, it is unclear whether common inherited genetic variants interact with somatic driver mutations to influence cancer risk and prognosis.
In this study, I analyse multi-cancer datasets to investigate germline by somatic interaction in cancer and to evaluate the role of inherited genetic variants on risk, prognosis, nearby gene expression, response to anti-cancer therapy and adaptive immune response in common cancers. I describe how the p53 poly(A) SNP, rs78378222 (17p13.1; TP53), interacts with p53 mutational status in tumours to influence cancer risk, response to therapy and prognosis in common cancers. I find that a known colorectal cancer risk locus at 10p14 (rs10795668; ATP5C1) interacts with KRAS mutational status in tumours to associate with colorectal cancer risk. I identify two loci at 15q26.2 (rs72767781; NR2F2-AS1) and 15q22.2 (rs11447843; VPS13C) associated with prognosis in early-stage colorectal cancer at genome-wide significance, together with numerous suggestive loci. In particular, rs184423256 (8q22.3; RRM2B) and rs114887409 (4p16.1; ABLIM2) interact with KRAS mutational status in colorectal cancer to associate with clinical outcomes. Furthermore, I identify 22 loci associated with infiltrating CD8+ T cell density in colorectal cancer, which are used to infer the causal relationship between adaptive immune trait and prognosis in early-stage colorectal cancer.
In summary, this study constitutes an integrative analysis of germline by somatic interaction on risk, biology, and prognosis of common cancers. The findings provide supportive evidence that inherited genetic variants can play an active role during tumour development, thus offering insight into the genetic basis of cancer susceptibility and practical guidance for personalised disease prediction.

Keywords: stratified GWAS
cancer prognosis
somatic driver mutations
cancer risk
p53 tumour suppressor
germline by somatic interaction
KRAS oncoprotein
adaptive immune response
inherited genetic variants
Advisor: Church, D
Bond, G
Extending the scope of covalent peptide-protein conjugation: from purification to expanded nanoassembly

The surprising discovery of intramolecular isopeptide bonds within Gram-positive bacteria pili and surface adhesins gave rise to the development of a new type of protein conjugation method, namely the Tag/Catcher system. Among the different kinds of Tag/Catcher platforms, SpyTag/SpyCatcher is the leading system with more than 200 articles utilising the technology due to the rapid and buffer-independent nature of the reaction. In this thesis, I have developed a purification method called Spy&Go to complement the SpyTag/SpyCatcher platform. Spy&Go enables the purification of proteins using SpyTag as the affinity peptide tag. Spy&Go thereby eliminates the dependence on extraneous tags for purification of proteins intended for SpyCatcher-based protein conjugation reactions. Spy&Go was developed by engineering SpyCatcher2.1, a fast reacting variant of SpyCatcher, to become SpyDock by removing reactivity whilst maintaining tight binding to SpyTag. The purity of proteins purified through Spy&Go was comparable to the purity of proteins purified by Ni-NTA using a polyhistidine tag. Subsequently, a different route for elution of SpyTag-proteins was explored by conferring pH-sensitivity to a SpyDock variant through the introduction of histidine residues at the SpyTag003-binding interface. With the combined effects of three histidine mutations, SpySwitch was developed, which can bind SpyTag003 at pH 8.0 and release at pH 5.0. SpyTag/SpyCatcher has been used to modularly multimerise proteins for vaccination, nanomedicine and making enzymatic nanoreactors. To extend the scope of SpyCatcher-based protein multimerisation platforms, I developed a Spy oligomerisation toolbox composed of SpyCatcher002 fused to coiled coils, to multimerise SpyTag-proteins into dimer, trimer, tetramer, pentamer, hexamer and heptamer assemblies. The SpyCatcher002-oligomers enable a rapid and scalable route to multimerise different proteins into defined assemblies. An agonistic nanobody against Death Receptor 5 was multimerised through SpyCatcher002-oligomers and showed a stoichiometry-dependent effect on breast cancer cell line apoptosis upon receptor activation.

Keywords: SpyCatcher
pH switch
Protein purification
Oligomerisation
Protein engineering
Advisor: Howarth, M
John Ashenden and the Scientia astrorum Mertonensis : with an edition of Ashenden's Pronosticationes

John Ashenden, who flourished between the years 1336and 1365, was a fellow of Merton College,Oxford, and an astrologer. In the later Middle Ages the science of the stars, or scientia astrorum, comprised both astronomy and astrology. Merton College is well known for the school of natural philosophy which prospered there in the first half of the fourteenth century. At the same time, a group of Merton fellows and their acquaintances specialized in the scientia astrorum. Ashenden’s writings are illustrative of the scholarship of this Merton circle. The circulation and copying of astronomical and astrological texts played a major part in their studies. Ashenden compiled a large Summa of astrological theory from nearly one hundred sources. He also made predictions on the basis of reputed influences of eclipses and planetary conjunctions. Coincidental events, which appeared to follow what he had predicted, greatly encouraged him. He composed his predictions out of academic interest rather than for personal gain. His writings continued to be read for 400 years; yet by the Age of Enlightenment his learning had lost its value. Ashenden’'s scholarship was indicative of the weaknesses of medieval scientific enquiry--it was mostly qualitative rather than quantitative;and assertions were never put to real experimental tests. Astrology had as much to do with theology as it had with science. The questions of determinism, natural causation,and numerological prophecy excited Oxford theologians. On these issues Ashenden stood on an orthodox middle-ground.

Keywords: astronomy
Scientia astrorum Mertonensis
Pronosticationes
medieval astronomy
John Ashenden
medieval
astrology
The examination of marriage ritual among selected groups in South India

This thesis is concerned with variations in the traditional Hindu marriage ceremony as practiced by the several Tamil-speaking castes on the east coast of South India, The primary objective is to survey the descriptions of marriage ritual which are available in the current literature, rather than to attempt a sociological analysis of any particular problem. The intention has been to organize and examine the existing material with a view to additional field research in person in the near future. In the following pages we point out several significant differences in the nuptial rituals as they are performed at different levels in the caste hierarchy and these facts are interspersed with a discussion of the relation of the marriage ceremony to South Indian ritual in general. Because information on this topic is relatively abundant, the area to be considered in detail has been limited to three districts of Madras State: South Arcot, Tiruchirappalli and Thanjavur.
Continued in thesis ...

Keywords: marriage ritual
caste
ritual
India
South India
Understanding the mechanism of Adenovirus endosomal escape

Adenoviruses (AdV) are non-enveloped dsDNA viruses that cause respiratory and gastrointestinal diseases and are commonly used as vaccine and gene therapy vectors. In order to replicate inside a host cell, AdV must first penetrate the endosomal membrane and gain access to the cytosol. A highly conserved amphiphilic alpha helix within AdV protein VI (pVI) has been proposed as the membrane-lytic factor that is necessary for endosomal escape. However, the precise mechanism of endosomal membrane disruption is uncertain. This investigation aimed to characterise pVI and investigate the contribution of different domains using several biophysical techniques and electron microscopy. Firstly, a purification protocol was developed for recombinant wild type pVI and two loss of function mutants. The three pVI proteins, along with a synthetic peptide composed of the suggested membrane-lytic domain of pVI, were then examined using circular dichroism and analytical ultracentrifugation in order to further understand their secondary structure and oligomeric state. The effect of pVI on liposomes was then investigated using dynamic light scattering and a dye release assay and visualised using electron cryo-microscopy (cryoEM). Finally, electron cryo-tomography (cryoET) was used to examine membrane disruption events in 3D. The activity of pVI constructs upon liposomes was observed to be highly dependent on the membrane composition, with phosphatidylethanolamine reducing the activity of pVI.

Keywords: protein structure
protein characterisation
liposomes
viral entry
protein purification
endocytosis
electron microscopy
adenovirus
Advisor: Grünewald, K
The annexation of populations: a new state strategy?

This thesis aims to analyse the extraterritorial naturalisation practices of Russia and Hungary to determine the states’ motivation and the domestic and international consequences of the policies. At the individual level, it remains a state’s legal prerogative to confer citizenship upon whomever it wishes consensually. When done to an extraterritorial collective, the practice can and has caused disputes between states. Russian and Hungarian state officials defend the practice by arguing the conferral of citizenship is a legal manifestation of a responsibility to privilege co-nationals, wherever they may reside. While this position cannot be entirely dismissed, it is argued that it lacks sufficient explanatory power and that strategic and instrumental motivations are fundamental to the practice. Research in International Relations has so far neglected to investigate citizenship policies from a strategic foreign policy perspective, a shortcoming this thesis seeks to address. Using a case study qualitative research design involving fifty-two interviews with political stakeholders and an official state discourse analysis, it shows that Russia and Hungary have made international and domestic gains by naturalising targeted populations in their contiguous states, which can be metaphorically described as an annexation of populations. The official state discourse from the leaders of Russia and Hungary relating to external populations and territory are found to exhibit similarities. This thesis offers an emotive analogue that the extraterritorial naturalisations are justified as a means to rectify perceived injustices at historical losses caused by external rivals. The significance of this study is that it informs our theoretical understandings of key concepts of International Relations by focussing on the implications of extraterritorial naturalisation on sovereign territorial integrity, the nation, (dual) citizenship and will interest constructivists and realists and those interested in international law.

Keywords: Citizenship
Realism
Constructivism
Politics
Power politics
State strategy
Hungary
Nationalism
Ethnicity
Extraterritorial naturalisation
Russia
Foreign policy
International Relations
Identity
Advisor: MacFarlane, N