VictorJuiz/thesis huggingface dataset:
Modelling and analysis of ecological interactions in microbial community based bioreactors

Microbial communities refer to a number of microorganisms living together. To-date, a number of naturally occurring microbial communities are used for engineering purposes, e.g. anaerobic digestion, and the construction of artificial communities opens the door to wider applications. In microbial communities, the ecological interactions between species (e.g. competition, predation and mutualism) play important roles. The purpose of this thesis is to explore (1) the implications of such interactions in a bioreactor in terms of productivity and stability, and (2) the inference of such interactions particularly in a complex microbial community in order to form a basis for further manipulation such as optimisation and control.
This work firstly studies the cases involving different microbial species at the same trophic level, with a particular focus on the potential of overyielding (the collective yield of multiple microalgae species, in terms of overall biomass abundance or a specific biomass component, is greater than that of any single species grown in the same system) in the poly-culture of microalgae arising from the complementary use of a key resource, namely light over the spectrum range of photosynthetically active radiation. Using a mathematical model, it is demonstrated that complementarity of light absorption alone does not guarantee overyielding; other factors such as the operational settings (e.g. loss rate of the bioreactor) and species traits (complementarity of light absorption spectra) can also affect the possibility and the degree of overyielding and even the co-existence of multiple species.

Advisor: Yang, A
Parallel states, public services, and the competition for legitimacy in Kosovo

Recent work has illustrated how ‘non-state actors’ can be active and effective governance providers, often at the expense of a state. This has expanded our understanding of the supply side of non-state governance. However, there remains little work on the demand side. How do the people navigate between these different providers? Why do they choose the services of one over another?
I argue that the answer rests on two factors: the level of group solidarity individuals are subject to and the unique characteristics of the services they are receiving. Groups are an important part of our social lives, but the extent to which we depend on them varies. I argue that external threats increase group solidarity, which then constrains how individual members decide between providers. Second, public services have different characteristics that influence how people relate to them. Education is collectively delivered and tied to a national identity; decisions depend on social norms. Healthcare is individual and immediate; decisions are rooted in trust. Justice varies between discreet civil cases where people can ‘shop’ between authorities to gain the ‘best’ outcome, and criminal cases, which can comprise highly visible, collective events with significant social pressure. Understanding how the factors of group solidarity and service characteristics intersect is key to understanding the demand-side of non-state governance.
Drawing on extensive fieldwork, this thesis examines these factors across two periods of competitive governance pluralism in Kosovo. During the first period, from 1989 to 1999, an Albanian ‘parallel state’ formed in opposition to Serbia and provided education, healthcare, and access to justice in ‘parallel’ to the services of Serbia. Following the 1999 war and the beginning of the UN administration, parallel authorities were then established in Kosovo’s remaining Serb-majority enclaves. Again, education, justice, and healthcare were provided in parallel to the formal Kosovar state.

Advisor: Gledhill, J
Friedrichs, J
Hydrophobic gating and functional annotation of ion channels

Ion channels are integral membrane proteins that facilitate the permeation of ions through lipid bilayers. By means of a molecular mechanism known as hydrophobic gating, these proteins can close their conduction pathway to ion flow without the need for steric occlusion. Hydrophobic gates pose a challenge in the analysis of novel ion channel structures, as they cannot be detected by measuring the physical dimensions of a channel pore. This thesis therefore presents the Channel Annotation Package (CHAP), an open-source software tool for the functional annotation of ion channel structures based on molecular dynamics (MD) simulation and capable of reliably indentifying hydrophobic gates. The cation-selective 5-HT3 receptor and the anion-selective glycine receptor served as test cases to demonstrate the utility of CHAP. The functional status of several recent structures of these two channels was determined through MD simulation and hydrophobic gates were identified in both receptors. Furthermore, a high-throughput survey of ion channel structures enabled by CHAP revealed that hydrophobic gates occur in ~20% of the ion channel structural proteome. Next-generation polarisable force fields were used to explore the importance of electronic polarisation in MD simulations of ion channels. Water molecules passing a hydrophobic gate experienced a significant reduction of their dipole moment, mirroring the behaviour of water in a liquid-vapour phase transition. Polarisable ions interacted more strongly with uncharged protein residues than simulations employing traditional additive force fields suggest. Incorporating polarisation effects will thus be an important aspect of future computational studies of ion channel structure and function. The impact of a transmembrane potential on the hydrophobic gate in the 5-HT3 receptor was studied through atomistic MD simulations. Electrowetting occured only at supraphysiological voltages, while at lower field strengths pore de-wetting effectively prevented ion permeation. The hydration response of the channel could be quantitatively described by a thermodynamic model that includes the influence of the charged amino acid residues of the channel protein. Electric field effects are unlikely to play an important role for hydrophobic gating in biological ion channels, but may potentially be exploited in the design of gated artificial nanopores.

Keywords: hydrophobic gating
ion channels
functional annotation
electrowetting
polarisable force fields
Advisor: Tucker, S
Sansom, M
Characterisation of PRC1 dynamics and chromatin binding in live cells

Development of complex multicellular organisms depends on precise spatiotemporal regulation of transcription of genes in the genome. Although this regulation is known to depend on sequence-specific transcription factors, chromatin modifying proteins have also emerged as key regulators of transcription in development. Polycomb proteins represent a class of well studied transcriptional repressors which assemble into two main complexes with histone-modifying activity, Polycomb repressive complexes 1 (PRC1) and PRC2. PRC1 exists in mammalian cells as multiple complexes of distinct subunit composition, formed around a catalytic core of an E3 ubiquitin ligase and one of six PCGF proteins, which monoubiquitylate histone H2A. In addition to dictating the level of catalytic activity of the complex, inclusion of a different PCGF protein results in incorporation of different chromatin-binding modules in each complex. Although previous work has established that enrichment of PRC1 at the promoters of target genes is required to achieve repression, how the mechanisms by which PRC1 subunits interact with chromatin contribute to targeting PRC1 to specific sites in the genome remains unclear.
In order to advance our understanding of how Polycomb proteins interact with the genome, I have employed live cell imaging and single particle tracking to characterise the dynamics and subnuclear localisation of PRC1. I discover that PRC1 subunits have broadly similar and dynamic behaviour, although a small fraction of molecules exhibit stable binding. Quantification of the numbers of PRC1 subunits reveals they are of relatively low nuclear concentration, despite their role in depositing H2AK119ub1 across the genome. Using systems in which I can remove PRC1 catalytic activity or induce degradation of a core PRC2 subunit, I demonstrate that PRC1 catalytic activity and PRC2 contribute modestly to PRC1 interactions with chromatin. Despite this modest change, I find that both are required for enriching Polycomb proteins at nuclear foci. I investigate the contribution of DNA binding of PCGF1-PRC1 subunit to the dynamics of both PRC1 and PCGF1, and find that it is not required for PCGF1 chromatin binding. I show, furthermore, that PRC1 stable binding and localisation within Polycomb bodies depends on specific PCGF proteins. Together, these observations provide a quantitative characterisation of PRC1 chromatin binding and localisation, and provide insights into the contribution of major chromatin-binding mechanisms to Polycomb dynamics.

Advisor: Klose, R
Modelling of arterial and haemogenic endothelium development from mouse and human pluripotent stem cells

One of the most promising objectives of clinical haematology is to derive transplantable autologous haematopoietic stem and progenitor cells (HSPCs) from human pluripotent stem cell (PSC) sources in vitro, but efficient and clinically relevant methodologies remain unavailable. Observations in the developing vertebrate embryo indicate that the haematopoietic stem cells (HSCs) capable of long-term engraftment are produced by the third and last wave of haematopoietic development. This occurs in the developing dorsal aorta (DA) from haemogenic endothelium (HE) in close association with an arterial vascular endothelial niche. Notch and Vascular endothelial growth factor A (VEGFA) signalling pathways are critical regulators of arterial identity and HSPC development.
To better understand the lack of engrafting HSCs in in vitro PSC differentiation protocols, we further characterised a previously published, serum-free murine embryonic stem cell (mESC) embryoid body (EB) differentiation system. Results showed lack of a robust arterial niche and Notch signalling, and production of HSPCs resembling the erythro-myeloid progenitors (EMP) normally detected during one of the earlier, extra-embryonic waves of haematopoietic development. We then showed that transiently culturing cells with high concentrations of VEGFA led to activation of an arterial programme in cultured cells, though this was insufficient to drive HSC differentiation. Importantly, we showed the haematopoietic potential of arterial delta-like 4 (DLL4) expressing cells depends on VEGFA concentrations in the culture, demonstrating the potential of arterial cells to become HE.
To adapt these findings to a more clinically-translatable setting, we also characterised a serum-free, monolayer-based system for the differentiation of human HSPCs previously developed in the lab, commercially available as STEMdiff™ Hematopoietic Kit. Similar to results in the murine system, the supporting niche showed limited arterial vascular endothelium differentiation and was instead primarily composed of mesenchymal stromal-like cells. Culturing cells in high concentrations of VEGFA markedly enhanced arterial endothelium formation throughout culture, and concurrently decreased mesenchymal stroma. Likewise, we observed the presence of immunophenotypic DLL4+ HE at early stages in cultures treated with high VEGFA concentrations, confirming data obtained from the mESC system. Despite lack of engraftment capacity of HSPCs, our studies contribute potential insights to the question of the haematopoietic potential of arterial endothelium. This will guide further improvement of currently available protocols to support in vitro HSPC differentiation.

Keywords: Arterial Endothelium
Pluripotent Stem Cells
Haematopoietic Stem and Progenitor Cells
Haemogenic Endothelium
Advisor: Porcher, C
Patient, R
Ego-motion estimation and localization with millimeter-wave scanning radar

In contrast to cameras, lidars, GPS, and proprioceptive sensors, radars are affordable and efficient systems that operate well under variable weather and lighting conditions, require no external infrastructure, and detect long-range objects. For these reasons, radar is a reliable and versatile sensor well suited for ego-motion estimation and localization. However, various radar artifacts and characteristics— including speckle noise, receiver saturation, multipath reflections, low spatial res- olution, and slow update speeds—make it an especially challenging sensor with which to work.
In this thesis, we present algorithms for radar-only odometry and localization for mobile autonomous systems. We focus primarily on odometry and show that our approach can be adapted for localization. Using a frequency-modulated continuous-wave (FMCW) scanning radar, we first extract keypoints from radar scans in a manner that avoids redundant returns, accounts for high levels of noise, and reduces reliance on the amplitude of received power as an indicator of occupancy. To estimate relative motion from the keypoint sets, we then perform scan matching by greedily adding point correspondences based on unary descriptors and pairwise compatibility scores in a graph matching framework.
Our pipeline achieves reliable and accurate ego-motion estimation under challenging conditions and across a range of settings. The pipeline of our most recent paper requires only one input parameter and no outlier detection, no model-reliant motion filters, nor any additional sensors. Our system operates well even in the absence of a motion prior and is highly robust to radar artifacts. We demonstrate its ability to match the performance of visual odometry and GPS/INS, remaining precise and robust even under difficult conditions that cause the latter two systems to fail. Additionally, it adapts effortlessly to diverse environments, from urban UK to off-road Iceland, achieving an average scan matching accuracy of 5.20 cm and 0.0929 degrees when using GPS as ground truth.

Keywords: Localisation
Radar
Odometry
Scanning radar
Frequency-modulated continuous-wave radar
Ego-motion estimation
Advisor: Newman, P
Arrangement, listening, and the music of Gérard Pesson

This thesis develops a critical framework for the study of musical arrangement and its relationship with concepts of listening through interpretations of music by Gérard Pesson (born 1958). It begins by identifying and accounting for persistent interpretative reflexes in existing discussions of arrangement, arguing that arrangement is best understood not as a type of musical object defined by fidelity to an original but rather as a way of listening influenced by this and other concepts. The four case studies that follow explore different implications of this shift in critical perspective, combining close reading and listening, philosophical reflection (in particular insights offered by conceptual metaphor theory and figures including Bergson, Sartre, and Adorno), and studies of reception. The first case study displaces the ‘original’ as the primary source of an arrangement’s significance, arguing that Nebenstück (1998) plays extensively on the meanings of medium, through the manipulation of timbre and noise. The second considers the idea of linear temporal fidelity to a source as an engagement with notions of structural listening, using an examination of Ambre Nous Resterons (2008) to demonstrate that such fidelity is not a condition of arrangement but an ideal from which arrangements might meaningfully depart. The third complicates the relationship between the timbral and temporal aspects of arrangement discussed in the previous two chapters, exploring how Pesson manipulates both aspects in Wunderblock (2005) to suggest the absence rather than re-presentation of a source. The fourth probes the fraught relationship between notions of arrangement, fidelity, and kitsch within the overlapping contexts of modernism and historical ‘authenticity’, analysing the discourses surrounding Kein Deutscher Himmel (1997) supplied by Pesson himself, the transcription’s commercial distribution, and a variety of its listeners. Finally, this thesis considers the extent to which musical arrangements, in particular those of Pesson, might be interpreted as offering ‘critical’ perspectives on listening.

Keywords: Pesson
Music
Couperin
Fidelity
Erasure
Transcription
Brahms
Noise
Arrangement
Metaphor
Adaptation
Kitsch
Gérard
Temporality
Bruckner
Listening
Recomposition
Mahler
Advisor: Grimley, D
Light-activated synthetic tissues

In this thesis, biological activity is recreated from the bottom-up. By putting together carefully-defined aqueous solutions of chemicals, the fundamental mechanisms of specific cells and tissues were replicated. Only one of the tissue’s functions was chosen for each construct. Of the billions of molecules inside each cell, only the necessary components were incorporated. Light was used to remotely control this biological function, either by using natural light-activatable molecules or by chemically-modifying others to yield them light-responsive. The recreated functions were image-detection, by imitating a retina, and signal propagation, by imitating a nerve. For this, artificial cells were formed from self-enclosed membranes, in which the contents were confined, and the membrane proteins reconstituted. The artificial cells were then assembled into artificial tissues, which bestowed them with their respective emergent properties, i.e. image detection and signal propagation. Droplet networks were used as the building blocks due to their modularity and bio-compatibility. The resulting light-activated droplet networks might pave the way towards synthetic interfaces with living tissues, or even the generation of organism-like constructs.

Advisor: Bayley, H
A study of the variability in the molecular structure of the human pancreas with age and its effect on islet isolation and transplantation outcomes

Pancreatic islet transplantation is a minimally invasive treatment that has the potential to reverse Type 1 Diabetes Mellitus in selected patients. Islets of Langerhans are isolated (extracted) from the pancreatic exocrine tissue using a collagenase and supplementary protease enzyme blend, which digests the extracellular matrix (ECM) scaffold surrounding human islets. However, the inefficiency of current enzyme blends to digest the pancreatic ECM from younger donors (those aged ≤35 years) has led to the underutilisation of donor pancreases from this age group. The hypothesis is that suboptimal digestion in younger donors is a likely consequence of age-related differences in the pancreatic ECM. However, this has not been previously studied in detail at the molecular level. The studies described in this thesis therefore aimed to define how the composition of the native pancreatic ECM is influenced by age and how this in turn affects the enzyme-mediated digestion of this structure.
Initially, the UK donor data set was analysed to determine the impact of different donor factors on islet isolation and transplantation outcomes. Whilst the success of islet isolation was clearly shown to increase with donor age, islets from younger donors demonstrated enhanced post-transplantation graft function.
High-throughput proteomics was then used to identify quantitative differences in native pancreatic matrix protein expression between younger (≤35 years old) and older (≥45 years old) donors. These novel studies identified substantial age-related differences in the pancreatic matrisome and demonstrated that a number of key matrix proteins, including several collagen and laminin chains, were significantly more highly expressed in younger donors.
Subsequently, the impact of donor age on pancreatic matrix digestion was studied through the development of a slide-based digestion assay. This involved the treatment of pancreatic tissue sections with collagenase and neutral protease, at clinically relevant concentrations. Following enzyme treatment, immunostaining was used to assess the digestion of specific matrix proteins. Once assay reproducibility was confirmed, this technique successfully demonstrated that age significantly influenced the digestion of several key matrix proteins. These results were confirmed by using Raman microspectroscopy (RMS) as a novel label-free technology to study ECM digestion. Furthermore, RMS indicated that age affected the action of collagenase to a greater extent than neutral protease.
The studies detailed in this thesis provide novel insights into the impact of donor age on the composition and digestion of the pancreatic ECM. Continued detailed analysis will aid in the development of targeted donor-specific enzyme blends to dramatically improve the overall efficiency of human islet isolation and transplantation.

Keywords: Human islet isolation
Collagenase
Extracellular matrix
Human islet transplantation
Collagen
Advisor: Johnson, PRV
Cros, SE
The development of catalytic methods for the synthesis of saturated nitrogen heterocycles

Chapter 1: Introduction
The introduction gives a description of the applications of azetidines, pyrrolidines and piperidines, as well as a brief overview of existing methods for their synthesis. Selected examples from the chemical literature are discussed. This chapter also reviews the history and development of hydrogen borrowing catalysis for nitrogen alkylation.
Chapter 2: Photoredox Catalysis for the Synthesis of Azetidines
The development of visible light mediated photoredox catalysis for azetidine synthesis was explored. A Ru(bpy)32+ catalyst system was employed to induce single electron reduction of 1 phenylbut 2 en 1 one and reaction of the resulting radical anion was attempted with a number of nitrogen containing electrophiles. Subsequently, a tethered substrate featuring an enone and an oxime portion was designed, synthesised and subjected to a screen of photoredox catalysts, with the hope of effecting an intramolecular azetidine formation.
Chapter 3: Hydrogen Borrowing Catalysis for the Synthesis of Piperidines
Hydrogen borrowing catalysis enabled the generation of a wide range of substituted piperidine scaffolds. Diols are employed as double alkylating agents and overall the process forms two new C–N bonds to furnish the heterocycle. A range of diols and amines were subjected to the reaction conditions to synthesis piperidines. The synthesis of pyrrolidines, azetidines and heterocycles bearing more than one heteroatom were also investigated under the hydrogen borrowing conditions.
Chapter 4: Stereoselective Synthesis of Piperidines using Hydrogen Borrowing Catalysis
Hydrogen borrowing catalysis for the synthesis of piperidines with stereogenic centres at the C2, C3 and C4 positions was investigated. The use of an enantiopure amine was explored for stereoinduction at the C2 centre. Through extensive optimisation, water was discovered to be an optimum reaction solvent and a new set of reaction conditions were developed enabling stereoretention in up to 93:7 er at the C3 position. Piperidines bearing a stereogenic centre at the C4 position could be synthesised from enantioenriched starting materials as this centre was found to be unharmed during the hydrogen borrowing reaction.
Chapter 5: Experimental
This chapter contains the experimental procedures and spectroscopic data for all of the compounds described within the thesis.
Chapter 6: Appendix
The X-ray crystallographic data for compound 240 can be found in the appendix.
Chapter 7: References
The references cited within the thesis can be found in this chapter.

Advisor: Donohoe, T