VictorJuiz/thesis huggingface dataset:
The impact of sequence diversity on the glycan shield of HIV-1 immunogens

Vaccine strategies for the human immunodeficiency virus type 1 (HIV-1) focus on the mimicry of its envelope spike (Env), due to its exposed location on the viral membrane and role in mediating infection. However, the virus has evolved to minimise the immunogenicity of Env, notably through extremely high sequence variability and the shielding of conserved protein epitopes by an extensive array of host-derived, immunologically ‘self’ N-linked glycans. Despite this, a subset of infected individuals eventually develop broadly neutralising antibodies that can recognise these glycans. Defining the composition of glycan epitopes on both viral Env and candidate immunogens is therefore a major research focus for HIV-1 vaccine design.
Using recombinant, soluble mimics of Env, this thesis sought to determine the impact of protein sequence on the processing of the glycan shield. This was addressed on three levels: the impact of virally-encoded sequence diversity, the impact of engineered stabilising mutations, and the impact of mutations affecting glycosylation sites. Despite the extensive diversity displayed by the Env sequence, many features of the glycan shield were remarkably conserved. Mutations affecting glycosylation sites, however, did impact the fine processing of nearby sites. Additionally, the glycan composition of Env mimics could be subtly altered using glycan-dependent broadly neutralising antibodies, either during the expression or purification stages. The latter effect appeared to be sequence-specific.
Although recombinant, soluble Env proteins are good structural and antigenic mimics of native, viral Env, the extent to which their glycan shields resemble that of infectious viruses is unknown. To that end, the glycosylation of a candidate immunogen was compared to that of sequence-matched Env derived from infectious virions. The glycan processing of key broadly neutralising antibody epitopes was largely conserved between virus and immunogen. However, there were subtle differences at some sites, with the viral material typically displaying elevated glycan processing. Given that recombinant Env constructs are good mimics of the viral glycan shield, they are likely also inherently immunoquiescent. Accordingly, this thesis also explored a strategy to boost the immunogenicity of the glycan shield, using yeast to decorate a soluble Env immunogen with ‘non-self’ glycan structures.
Overall, features of the Env glycan shield are largely conserved between virus and immunogens, and across multiple genotypes, supporting it as a suitable target for HIV-1 vaccine design.

Keywords: mass spectrometry
immunogens
N-glycosylation
HIV-1
vaccine
Advisor: Crispin, M
Wormald, M
The role of macrophages in the host response to radiation

Emerging pre-clinical data suggests a role for radiation in eliciting antitumor immunity. Effective anti-tumour responses can be hindered by highly immunosuppressive tumour microenvironments. We aimed to investigate the role of macrophages in the immune response to radiation.
We used the murine colorectal cancer cell line MC38 and the pancreatic cell line KPC for in vitro and in vivo work. To examine the immune response following irradiation, subcutaneous xenografts were analysed by flow cytometry. Further characterisation of macrophages was carried out by gene expression analyses of RNA from isolated cells, along with ex-vivo functional assays. To determine the effect of macrophage depletion, we used an antibody targeting macrophage colony stimulating factor (CSF-1).
Single dose 10Gy irradiation to murine tumors, generated from colorectal (MC38) and pancreatic (KPC) cell lines induced Colony Stimulating Factor 1 (CSF-1). Coincident with the elevation in CSF1, CD11b+ F480+ macrophages increased in the tumors, peaking five days following irradiation. These tumor-associated macrophages (TAMs) from irradiated tumors were skewed toward an immunosuppressive phenotpye (CD206hi iNOSlo) and were more effective in suppressing CD8 T cell expansion ex vivo.
Macrophage depletion via anti-CSF (aCSF) reduced macrophage numbers yet only achieved tumor growth delay when combined with radiation. The tumor growth delay from aCSF after radiation was abrogated by depletion of CD8 T cells. There was enhanced recognition of tumor cell antigens by T cells isolated from irradiated tumors, consistent with increased antigen priming. Radiation stimulated increased expression of PD-L1 on tumor cells, limiting antitumor responses. The addition of anti-PD-L1 resulted in improved tumor suppression and even regression in the highly resistant murine pancreatic cancer model.
In summary we show that adaptive immunity induced by radiation is limited by the recruitment of highly M2 polarised immunosuppressive macrophages. Macrophage depletion with aCSF partly reduced the immunosuppression after radiation, but additional treatment with anti-PD-L1 was required to achieve tumor regression.

Advisor: Muschel, R
Developing anti-p53/HLA-A*0201 T-cell receptor mimic antibodies for cancer immunotherapy

T-cell receptor mimic (TCRm) antibodies target a dual antigen epitope consisting of a peptide derived from an intracellular protein, and the major histocompatibility complex class I (MHC-I) molecule that presents the peptide at the cell surface. As traditional antibodies typically target cell surface or secreted antigens, TCRm antibodies advantageously expand the range of targetable antigens to include peptides derived from intracellular proteins.
This thesis describes the development of TCRm antibodies targeting peptides that are derived from the wild type p53 protein and are presented by human leukocyte antigen (HLA)-A2. We further characterised the specificity and safety of the T1-116C TCRm antibody, which was the most extensively studied TCRm antibody in the laboratory prior to the start of this DPhil project. We showed that T1-116C labels primary AML and myeloma cells. We investigated the specificity of the T1-116C TCRm antibody for the p5365-73 peptide, RMPEAAPPV, by substituting each amino acid within the peptide individually, and showed that T1-116C recognises multiple tumour antigens. Using in silico analysis we identified 271 potentially cross-reactive peptides. We tested a panel of 25 peptides that are conserved in mice in vitro, showing that T1-116C binds peptides derived from a broad range of normal tissues. Despite these findings, in vivo testing of T1-116C cross-reactivity in human HLA-A2 transgenic mice demonstrated that T1-116C does not cause toxicity to normal mouse tissues.
We also generated chimeric antigen receptors (CARs) for T-cell therapy using the single chain variable fragment of p53-targeting TCRm antibodies to provide the CAR specificity. We found that the CAR derived from T2-2A, a TCRm antibody that targets the p53187-197 peptide, GLAPPQHLIRV, demonstrated superior specificity for target peptide-HLA-A2 tetramers and cell lines to the T1-116C CAR. Through these studies, the T2-2A TCRm antibody has emerged as a potential therapeutic agent when used in the CAR format.

Keywords: p53
MHC class I presented peptide
Cancer immunotherapy
Therapeutic antibody
T-cell receptor-like (TCR-like) antibody
T-cell receptor mimic (TCRm) antibody
HHD mouse
CAR T-cell
T-cell epitope
p53 peptide
Advisor: Li, D
Banham, A
Hope, fear, and conceptions of the future in the early Principate

This thesis examines a selection of ways in which Roman political actors (be they senators, equites, troops, plebs or others) conceived of the political future of Rome, in a series of four crises from the Ides of March 44 BCE to the establishment of the Flavian dynasty in 69 CE, and the way in which contemporary and later authors represented the views of those figures in historical narratives. It demonstrates that there was a great deal of uniformity in the political language used in these crises, first, by those who sought to restore the consular government that had existed prior to the supremacy of Julius Caesar; secondly, by those who sought to promote and maintain the Julio-Claudian family’s exceptional position attained after the civil wars; and thirdly, by those who sought some form of compromise, perhaps in the form of a more virtuous princeps, or the devolution of some authority to the senate, as ‘the Principate’ developed from an ad hoc bundle of powers into a ‘system’ of government. There was often a strong moralising element in this political discourse, and it centred on the virtues and vices of leaders involved in the crises. In many cases these individuals came to embody competing images of the future in their own right, as in the case of Antony and Octavian, the successors to Augustus, or the rival contenders in 68-9 CE. In other cases, slogans such as libertas could encapsulate idealised images of the future in a synecdochic manner, and acted as rallying points for political action. Hopes for a better future were often contrasted with fears of some other outcome, and the two were often presented as a dichotomy, to exhort audiences in a particular direction. Unrealised visions of the future and the failed plans that went along with them shaped the political landscape of Rome and its development in a range of important ways, and continued to be influential as a part of Roman cultural memory and historiography.

Advisor: Clark, A
Clarke, K
Effect of adenovirus infection on hypoxia inducible factor 1 pathway

Low oxygen (hypoxia) and stabilisation of the Hypoxia-Inducible Factor 1 alpha (HIF-1α) have been reported to be either beneficial or detrimental to the efficacy of candidate oncolytic viruses such as reovirus, vesicular stomatitis virus or Newcastle disease virus. We have found that Enadenotucirev (an oncolytic group B adenovirus) has increased activity in hypoxia compared with normoxia. In order to understand how hypoxia benefits EnAd, we studied the HIF-1 pathway during virus infection.
Here we have shown that EnAd infection leads to down-regulation of the HIF-1α protein in certain virus-permissive cell lines in hypoxia. We also report a similar effect after infection with wild type adenoviruses (Ad5 and Ad11). To determine the mechanisms underlying this downregulation, we measured the mRNA levels of HIF-1α and its target genes by reverse transcription quantitative PCR and found that all three viruses down-regulate HIF-1α transcripts in both normoxia and hypoxia. We also found that this down-regulation is independent of the proteasome complex.
Our data has also shown that AD293 cells (which have Ad5 E1 gene) have lower basal levels of HIF-1α protein compared to other cell lines. Since several studies suggest that adenovirus E1A regulates many cellular genes, we speculate that adenovirus mediated down-regulation of HIF1α mRNA is achieved by E1A. Future work will look at the role of E1A in regulating the HIF-1 pathway.

Advisor: Seymour, L
Fisher, K
Who governs now? The politics of power in the applied sciences NYC initiative

This thesis explores the politics of power in the policy decision-making processes of Applied Sciences NYC, an economic development initiative under the administration of Mayor Michael Bloomberg (2002–2013) in New York City. I seek to understand the politics of power in policy decision-making processes of both data-driven governance and public participation. The literature on the politics of power in public policy decision-making processes does not adequately address public policy decision-making processes of both public participation and data-driven governance. What power dynamics explain the policy decision-making processes in Applied Sciences NYC? And, given the norm of data-driven policy decision-making under the Bloomberg administration and the Applied Sciences NYC power dynamic, why also include public participation in the policy decision-making processes of Applied Sciences NYC?
New York City governmental officials intimated and publically professed that a multiplicity of non-governmental actors possessed power in the policy decision-making processes of Applied Sciences NYC. Via process-tracing methodology, I provide nuance to this suggestion of pluralist power. I observe that mayoral agency—and in particular the mayor’s definition of economic development, his norm of data-driven policy decision-making, and his personal background—played a decisive role in the policy decision-making processes of Applied Sciences NYC. In so doing, mayoral agency closed the policy decision-making processes of Applied Sciences NYC such that only certain ideas were considered and only certain participants were included. I maintain that New York City governmental officials nonetheless included processes of public participation in Applied Sciences NYC with three primary goals: to generate ideas and validate their hypotheses; to mitigate future criticism; and to catalyze support. These research findings may inform conversations on public trust, openness, and inclusivity in American democracy. Further empirical work is necessary to understand if my findings with regard to power dynamics in the policy decision-making processes of Applied Sciences NYC also apply to other cases.

Advisor: Ebbinghaus, B
The history and viability of constitutivism in ethics

The topic of this thesis is constitutivism in ethics: its history and its viability. Constitutivists hope to show that moral standards are normative because if we are not following them, we are failing to be agents. We cannot escape trying to be agents: it is just our way of trying to do anything in particular. In failing to be agents, then, we are failing to do what we ourselves are trying to.
The force of normativity, on a constitutivist view, turns out to be the force of our own efforts to do things. Moral or pro-moral standards are what we must be guided by for our own attempts to do things to be internally consistent. The immoral would-be agent, then, is one who is divided against themself. They are trying to do the impossible: to be agents in a way that agents cannot.
Defending the viability of constitutivism – one half of my topic – only takes defending one form of it. This thesis focuses on Kantian constitutivism, which may be the most promising kind of it. It focuses in particular on Christine Korsgaard’s version of that position, as presented in The Sources of Normativity, Self-Constitution, her recent Fellow Creatures, and a range of essays.
The four substantive chapters of this thesis set out to answer four different questions. The first is what the components of Kantian constitutivism are. Two of those four components are claimed to be characteristic of constitutivism in ethics, and the chapter points to the historical background of all four of them. The second question is in what sense we face the problem of agency. The chapter first distinguishes rational and nonrational agency. It then explains how, on the view, rationality is self-conceptual, and attempts to pin down this talk of problem-facing.
The final two chapters of this thesis take up two closely related questions. These are why our moral psychology should feature what Kant calls “incentives,” and why, as Kant and Aristotle believe, it should feature not just acts, but ends. It argues that on the Kantian constitutivist picture, there are two demands on a moral philosophy of action. Those demands can be seen to generate the functional concepts of incentives and, via the steps of a Kantian moral argument, ends.

Keywords: Constitutivism
Immanuel Kant
Plato
Christine Korsgaard
Kantian ethics
Advisor: Hills, A
Essays on the new financial landscape

This dissertation consists of three essays, each examining the implications of a major change to the financial landscape over the past decade.
In the first essay, I show that price formation for cryptocurrencies is markedly different from that for other asset classes. I study two distinctive characteristics of cryptocurrencies. First, the blockchain structure of cryptocurrency means that there is a limit on the number of transactions that can be settled in any given time. Second, as a cryptocurrency is a form of money not backed by any asset class, its value depends on the extent to which it is used as a means of payment. Taken together, these characteristics mean that speculative activity can crowd out payment usage. Trading can lower the price of the asset, even when it is buy-side trading. I show that this may explain high price volatility.
In the second essay, we propose a novel channel for credit crunches. A borrower fears that there will be distress in the financial sector, in which case her relationship lender may not be able to finance her project. To insure against this risk, she chooses a smaller project that uninformed outsiders would be willing to finance. Financial distress therefore leads to lower investment, but not via the usual supply or demand side channels. We show that a small increase in distress risk can lead to a large downward jump in investment. This is joint work with Alan Morrison and Joel Shapiro.
Finally, the third essay examines how derivatives trading networks are affected by the introduction of mandatory central clearing. There can be a trade-off: central clearing can increase the mean of net exposures, but reduce the variance. We show that the trade-off can never be in the other direction. This suggests that, the more risk-averse agents are, the beneficial central clearing is likely to be. This is joint work with Rodney Garratt.

Keywords: CCP
cryptocurrency
global games
relationship lending
networks
credit crunch
blockchain
Advisor: Morrison, A
Shapiro, J
G-structures and superstrings from the worldsheet

G-structures, where G is a Lie group, are a uniform characterisation of many differential geometric structures of interest in supersymmetric compactifications of string theories. Calabi–Yau n-folds for instance have torsion-free SU(n)-structure, while more general structures with non-zero torsion are required for heterotic flux compactifications. Exceptional geometries in dimensions 7 and 8 with G = G2 and Spin(7) also feature prominently in this thesis.
We discuss multiple connections between such geometries and the world- sheet theory describing strings on them, especially regarding their chiral symmetry algebras, originally due to Odake and Shatashvili–Vafa in the cases where G is SU (n), G2 and Spin(7). In the first part of the thesis, we describe these connections within the formalism of operator algebras. We also realise the superconformal algebra for G2 by combining Odake and free algebras following closely the recent mathematical construction of twisted connected sum G2 manifolds. By considering automorphisms of this realisation, we speculate on mirror symmetry in this context.
In the second part of the thesis, G-structures are studied semi-classically from the worldsheet point of view using (1, 0) supersymmetric non-linear σ- models whose target M has reduced structure. Non-trivial flux and instanton- like connections on vector bundles over M are also allowed in order to deal with general applications to superstring compactifications, in particular in the heterotic case. We introduce a generalisation of the so-called special holonomy W-symmetry of Howe and Papadopoulos to σ-models with Fermi and mass sectors. We also investigate potential anomalies and show that cohomologically non-trivial terms in the quantum effective action are invariant under a corrected version of this symmetry. Consistency with supergravity at first order in α' 0 is manifest and discussed. We finally relate marginal deformations of (1, 0) G 2 and Spin(7) σ-models with the cohomology of worldsheet BRST operators. We work at lowest order in α' 0 and study general heterotic backgrounds with bundle and non-vanishing torsion.

Advisor: de la Ossa, X
Folding pathways of DNA nanostructures

DNA origami is a robust technique for the production of DNA whereby a long scaffold strand is folded through interactions with many short staple strands. This thesis describes my work on two DNA origami-based systems. One is an origami tile whose folding can be kinetically-controlled through the use of helperstrands′,whicharedesig≠d→b∈d→thescaffold.Thisallowstheti≤→befoldedraπdlyattemperaturesbelowtheti≤me<∈gtemperature,whichis¬otherwisepossib≤due→theformationandpersistenceofoff-tar≥tstap≤-template∫eractionsatsuchtemperatures.Omissionofse≤ctedhelperschan≥sthefold∈gpathwayoftheti≤;thismayallowtheuseofhelperstrands→prime' a template to preferentially fold with a specific staple set in a mixture of different staple sets.
The second system is a novel `origami-like' structure in which the equivalent of the scaffold and staples are both double-stranded structures which interact through DNA T-motifs. This differs from conventional origami in that: a) binding domain sequences are reused, and b) the interactions which govern folding (T-motifs) are less stable than the staple-template hybridisations used in conventional origami.
The structure I designed uses only four unique binding domains (seven copies of each) and two types of l∈ker′(≡a≤nt→stap≤s),whichmeanstherearealar≥νmberofpotentialstructureswhichcod̲form.Desπtethis,fold∈gofthetar≥tstructurewasseenatr∞mtemperature,sug≥st∈gt
ˆ
o
ff-tar≥t∫eractionscanbereversedatthesetemperatures→allowthestructure→reachitsminiμmeee≠rgy.Chang∈gtheidentityofonlyo≠ofthel∈kersrest̲s∈fold∈gofad⇔erenttar≥tstructure.TheseT-motif origami' structures can be used to investigate the minimum number of unique binding domains required to specify a structure, and for applications which require reconfigurability.
Both systems were characterised using gel electrophoresis and AFM imaging.

Advisor: Turberfield, A
Bath, J