VictorJuiz/thesis huggingface dataset:
Design of a ratiometric reporter to improve the dynamic range and sensitivity of a bacterial biosensor
Keywords: fluorescence
Microbial
bacteria
microbiology
ratiometric
Biosensor

For applications from biosensor generation to synthetic biology, the ability to accurately and quantitatively generate input-output data from biological systems over a wide dynamic range is becoming increasingly important. This study has demonstrated that a simple approach utilising multiple promoters, recognising the same transcriptional activator but with differing affinities, linked to compatible reporter genes can achieve this goal. This simple system highlights that even for complex promoters with multiple binding sites we can use the ratio of two reporters to obtain accurate and reproducible input-output data for reporters contained on a high copy number plasmid without the need for any background subtraction or accurate determination of cell number. It has also demonstrated that the precise promoter strengths are not too crucial to the design, provided they are significantly different, as taking the ratio of either the high affinity/low affinity or medium affinity/low affinity channels give similar improvements over any single channel alone.
The modularity of this system means that it should be possible to exchange the IPTG inducible promoter and hence place the ntrC* gene under the regulation of any environmentally important promoter.
It should also be possible to simply construct different strength promoters for the same transcriptional activator by standard DNA synthesis techniques, therefore allowing direct ratiometric detection of specific active transcription factors. Finally, there is considerable interest in the biosensor field in the use of immobilised cells for field based applications. In these cases, determining the exact number of viable cells present at the time of use may be problematic and obtaining high signal levels may also be essential. In this regard, the use of ratiometric reporters from constructs on high copy number plasmids could alleviate many of these potential problems and significantly simplify the required biosensor detection equipment.
Genetic control of the olive fruit fly, Bactrocera oleae
Keywords: tephritid
olive fly
autocidal
sterile insect technique
transgenic
RIDL

The olive fruit fly, Bactrocera oleae, (Rossi) (Diptera:Tephritidae), is a key pest of olive crops. The sterile insect technique (SIT) is an environmentally benign and species-specific method of pest control, aiming to reduce the reproductive potential of a wild population through the mass-release of sterile insects. Previous olive fly SIT trials, involving the release of gamma-ray sterilised mixed-sex populations, achieved limited success. Key problems included altered diurnal mating rhythms of the laboratory-reared insects, leading to assortative mating between released and wild populations, and low competitiveness of the radiation sterilised mass-reared flies. Consequently, the production of competitive, male-only release cohorts is seen as essential.
The RIDL (Release of Insects carrying a Dominant Lethal) system is a transgene-based derivative of SIT, one version of which involves the mass release of insects carrying a female specific lethal transgene (fsRIDL). This thesis describes: 1) the development of fsRIDL olive fly strains and the molecular analysis of transgene insertion and function; 2) the analysis of strain life-history parameters; 3) studies into sexual selection and mating compatibility; 4) a caged proof-of-principle population suppression trial; and, 5) selection dynamics on the fsRIDL trait in caged populations.
Olive fly fsRIDL strains were developed with full female-lethal penetrance and repressibility. The lead strain displayed similar life-history and sexual competitiveness traits to those of the wild-type strain from which they were derived. In addition, transgenic males showed photoperiod compatibility and strong sexual competitiveness with field-collected wild olive flies. The feasibility of the fsRIDL approach was demonstrated when repeated male releases caused eradication of caged olive fly populations. Although needing field confirmation, these results suggest that fsRIDL olive fly strains may help to mitigate key problems experienced in previous olive fly SIT trials, and could help form the basis of a renewed effort towards olive fly SIT control.
Social sharing of emotions on individual, dyadic, and group levels
Keywords: social sharing
co-rumination
social networks

People turn to others for help and advice during hard times. Early psychologists suggested a ‘talking cure’ as a remedy for emotional turmoil (e.g., Freud, 1916–7/1963; Rogers, 1942). Likewise, folk psychology often sees heart-to-heart conversations as a win-win proposition that brings relief to the afflicted person and reinforces social bonds at the time of need. However, talking about problems does not always help (e.g., Rimé, 2009; Rimé, Mesquita, Boca, & Philppot, 1991; Rimé, Philippot, Boca, & Mesquita, 1992; Rose, 2002). In some cases, problem-talk can be a lose-lose proposition that drags both discussants into depression (Rose, 2002; Rose, Carlson, & Waller, 2007). This thesis examines co-rumination (Rose, 2002), a case of emotional sharing that hurts people instead of helping them, on three levels of analysis (individuals, dyads, and groups).
At the individual level, I sketch the life course of co-rumination and replicate earlier findings of gender differences. Furthermore, online survey data (N = 464) links co-rumination with agreeableness and neuroticism. I also demonstrate that co-rumination can be assessed with a brief measure that is 66% shorter than the original. At the dyadic level, data from recorded conversations between romantic couples show that face-to-face co-rumination influences people’s real-time emotional trajectories in complex ways. Furthermore, observer-ratings of the conversations suggest that third-parties can detect co-rumination, even from silent videos. Finally, I study how people react to others’ negative mood and co-rumination in a real social context by longitudinally following two cohorts of students and modelling their interactions with social network analysis tools. These models show that co-rumination appears to elicit social rejection from others, implying a possible pathway to depression via loneliness imposed on the co-ruminators.
Computational studies of transmembrane helix insertion and association
Keywords: potential of mean force
transmembrane helix insertion
membrane proteins
molecular dynamics

Membrane proteins perform a variety of functions essential for the viability of the cell, including transport and signalling across the membrane. Most membrane proteins are formed from bundles of transmembrane helices. In this thesis molecular dynamics simulations have been used to investigate helix insertion into bilayers and helix association within bilayers. The potentials of mean force for the insertion of helices derived from the cystic ﬁbrosis transmembrane conductance regulator into lipid bilayers were calculated using coarse-grained molecular dynamics simulations. The results showed that the insertion free energy increased with helix length and bilayer hydrophobic width. The insertion free energies obtained were signiﬁcantly larger than comparable quantities obtained from translocon- mediated insertion experiments, consistent with a variety of previous studies. The implications of this observation for the interpretation of in vivo translocon-mediated insertion experiments, and the function of the translocon, are discussed.
Coarse-grained and atomistic molecular dynamics simulations of the transmembrane region of the receptor tyrosine kinase EphA1 suggested that the transmembrane helix dimer was most stable when interacting via the glycine zipper motif, in agreement with a structure obtained by NMR spectroscopy. Coarse-grained simulations of the transmembrane region of EphA2 suggested that the dimer has two stable orientations, interacting via a glycine zipper or a heptad motif. Both structures showed right-handed dimers, although an NMR structure of the transmembrane region of EphA2 shows a left-handed dimer interacting via the heptad motif. Both structures obtained from coarse-grained simulations proved unstable when simulated at an atomistic level of detail.
The potentials of mean force for dissociating the EphA1 and EphA2 dimers were calcu- lated using coarse-grained molecular dynamics calculations. Convergence of the detailed structure of the proﬁles was not conclusively shown, although association free energies cal- culated from the proﬁles were consistent over a variety of simulation times. The association free energies were slightly larger than experimental values obtained for comparable sys- tems, but consistent with similar computational calculations previously reported. However, direct comparisons are difﬁcult owing to the inﬂuence of environmental factors on reported association free energies. The potential of mean force proﬁles showed that the interaction via the glycine zipper motif for EphA1 was signiﬁcantly more stable than any other confor- mation. For EphA2 the potential of mean force proﬁles suggested that interaction via the glycine zipper and heptad motifs both provided stable or metastable conformations, with the interaction via the glycine zipper motif probably at least as stable as that via the heptad motif.
Classical lyricism in Italian and North American 20th-century poetry
Keywords: Ezra Pound
Sappho
Classics
Catullus
20th-Century
Salvatore Quasimodo
Anne Carson
lyric
American poetry
translation
Classical Tradition
Giovanni Pascoli
Italian poetry
Greek
Latin

This thesis defines ‘classical lyricism’ as any mode of appropriation of Greek and Latin monodic lyric whereby a poet may develop a wider discourse on poetry. Assuming classical lyricism as an internal category of enquiry, my thesis investigates the presence of Sappho and Catullus as lyric archetypes in Italian and North American poetry of the 20th century.
The analysis concentrates on translations and appropriations of Sappho and Catullus in four case studies: Giovanni Pascoli (1855-1912) and Salvatore Quasimodo (1901-1968) in Italy; Ezra Pound (1885-1972) and Anne Carson (b. 1950) in North America. I first trace the poetic reception of Sappho and Catullus in the oeuvres of the four authors separately. I define and evaluate the role of the respective appropriations within each author’s work and poetics. I then contextualise the four case studies within the Italian and North American literary histories. Finally, through the new outlook afforded by the comparative angle of this thesis, I uncover some of the hidden threads connecting the different types of classical lyricism transnationally.
The thesis shows that the course of classical lyricism takes two opposite aesthetic directions in Italy and in North America. Moreover, despite the two aesthetic trajectories diverging, I demonstrate that the four poets’ appropriations of Sappho and Catullus share certain topical characteristics. Three out of four types of classical lyricism are defined by a preference for Sappho’s and Catullus’ lyrics which deal with marriage rituals and defloration, patterns of death and rebirth, and solar myths. They stand out as the epiphenomena of the poets’ interest in the anthropological foundations of the lyric, which is grounded in a philosophical function associated with poetry as a quest for knowledge. I therefore ultimately propose that ‘classical lyricism’ may be considered as an independent historical and interpretative category of the classical legacy.
“One of the Most Penetrating Minds in England:” Gerald Heard and the British Intelligentsia of the Interwar Period
Keywords: Pacifism
Aldous Huxley
1930s
Henry FitzGerald Heard
Dartington Hall
Gerald Heard

Gerald Heard (1889-1971) was an influential figure among the intelligentsia of the 1930s, once described by E. M. Forster as “one of the most penetrating minds in England.” However, he remains an ill-defined footnote, a marginal figure whose influence and reputation, although acknowledged, remains unexamined. This dissertation examines his life and work, and considers the role which Heard, as a generaliser and public intellectual, played in the intellectual landscape of the 1930s.
Central to Heard’s philosophy was a belief that society was in need of a spiritual and psychological force which could allow isolated individuals to participate in community with one another. Heard’s solution to bring about this evolution of consciousness would prove to be partly psychological, partly mystical and partly down to the product of a particular way of living. The first chapter outlines Heard’s philosophy in detail. Subsequent chapters are structured so as to provide a loose biographical chronology, each focussing on a different phase of Heard’s career and examining the development of his thought. Running throughout the dissertation is a consideration of Heard’s role as a public intellectual. It was as a popular ‘generaliser’ of thought that Heard found his public, and the limited degree of success he found as a man of action could be seen to be a natural limitation of the role he had constructed for himself.
Chapter II focuses on Heard’s time as personal secretary to Sir Horace Plunkett, father of the Irish Co-Operative Movement, and how the ideals of this movement can be seen to inform his developing ideas of human community. Chapter III looks at Heard’s role as a broadcaster with the B.B.C., where he became a noted populariser of science, firmly establishing himself as a public figure and cultural authority. It is arguably this increased public profile which provided Heard with a ‘public’ to whom he could address his ideas. Chapter IV, drawing on archival material from Dartington Hall, considers Heard’s role as a lecturer at Dartington School, and more importantly his first experiment to establish a small ‘group’ for meditation in an attempt to discover the mystical and psychological basis for a co-operative society. Chapter V examines his career as an outspoken pacifist, where he would advance his arguments for a radical reorganisation of society as a practical solution to the question of peace and further attempt to become a man of action.
Centralisers and amalgams of saturated fusion systems
Keywords: saturated fusion systems
finite group theory

In this thesis, we mainly address two contrasting topics in the area of saturated fusion systems. The first concerns the notion of a centraliser of a subsystem E of a fusion system F, and we give new proofs of the existence of such an object in the case where E is normal in F. The second concerns the development of the theory of `trees of fusion systems', an analogue for fusion systems of Bass-Serre theory for finite groups. A major theorem finds conditions on a tree of fusion systems for there to exist a saturated completion, and this is applied to construct and classify certain fusion systems over p-groups with an abelian subgroup of index p. Results which do not fall into either of the above categories include a new proof of Thompson's normal p-complement Theorem for saturated fusion systems and characterisations of certain quotients of fusion systems which possess a normal subgroup.
Evolution of PHDs as oxygen sensors: mechanistic and structural studies of the PHD of Trichoplax adhaerens, the simplest animal, and mechanistic studies of a PHD-like enzyme of the protist Monosiga brevicollis 
Keywords: crystal Structure
evolution
Monosiga brevicollis
PHD
oxygen Sensing
Trichoplax adhaerens

This work aimed to investigate the evolutionary origin of the involvement of the HIF Prolyl Hydroxylases (PHDs) in oxygen sensing. The α/β-heterodimer HIF (Hypoxia Inducible Factor) is a master regulator of oxygen homoeostasis in metazoans. In the nucleus, HIF binds to the Hypoxia Responsive Elements and forms a transcriptional complex that activates the transcription of a multitude of downstream genes. Under normoxic conditions, the Fe(II)- and oxygen-dependent PHDs catalyse 4R-prolyl-hydroxylation of the HIF α-subunit, which subsequently leads to its degradation.
It had previously been proposed that the evolution of the HIF-pathway, shared by all metazoans but not found in other organisms, is linked to the rapid diversification of multicellular life during the Cambrian Explosion. This work investigates the structural and biochemical properties of a PHD of the basal metazoan Trichoplax adhaerens (taPHD), and a PHD-like enzyme of the protist Monosiga brevicollis (mbP4H).
Two crystal structures of taPHD were obtained (1.2-1.3 Å), one containing a Trichoplax adhaerens HIFα subunit peptide (taODD). Comparison with crystal structures of human PHD2 showed a high degree of conservation of structural features and enzyme-substrate interactions. The prolyl-residue of taODD, shown to be hydroxylated by taPHD, is occupying the C4-endo conformation in the crystal structure, supporting the previously proposed mechanism of HIFα hydroxylation by PHD2 in humans. A conservation of biochemical properties with human PHD2, such as the formation of a stable enzyme-Fe(II)-2OG complex, was observed and could therefore be key to oxygen sensing by the PHDs.
mbP4H was shown to catalyse 4R-prolyl-hydroxylation of taODD. It was proposed that the native substrate of mbP4H is a protein containing a prolyl-hydroxylation site similar to taODD, possibly with a YXXLAP motif. The study of biochemical properties and substrate selectivity of mbP4H suggests that the precursor of PHDs may have had similar properties to mbP4H. Further work on mbP4H could therefore yield clues about the evolutionary origin of HIF-prolyl hydroxylases in oxygen sensing and probe the previously proposed connection between metazoan life and HIF–mediated oxygen sensing.
High resolution spectroscopy of open shell clusters
Keywords: van-der-Waals
microwave
spectroscopy

The microwave spectrum of the open-shell van der Waals complex NO-HF has been recorded in the region 6-20GHz using a pulsed nozzle Fourier transform microwave spectrometer. This is the first observation of the microwave spectrum of a open-shell van der Waals complex between two molecules. The spectrum exhibits a rich hyperfine structure with the observation of intermolecular hyperfine interactions in an isolated system providing a sensitive probe of electron transfer in the complex.
The spectrum consists of four fine structure transitions 5/2(e)-3/2(e), 3/2(e)-1/2(e), 5/2(f)-3/2(f), 3/2(f)-1/2(f) which have been fitted to a semi-rigid Hamiltonian developed to include the effects of the orbital and spin angular momenta of the unpaired electron on NO. A new treatment to account for the intermolecular hyperfine interaction was developed. The structure of the complex has been determined and is significantly bent with an angle of between 37 degrees and 49 degrees between the NO internuclear axis and the a-axis of the complex. The Renner-Teller parameter, epsilon 2, is very large and negative having the value of -10 449.32(4)GHz indicating that configuration with the unpaired electron in the plane of the complex is more stable.
The analysis of the hyperfine interactions of the hydrogen and fluorine nuclei uses two constants for each nucleus, one for the spatial relationship between the magnetic moments of the unpaired electron and the nuclear magnetic moment and a Fermi-contact term.
The Fermi-contact term for hydrogen is the first strong evidence of intermolecular charge transfer in an isolated van der Waals molecule.
Computational methods for the study of immunoglobulin aggregation
Keywords: Molecular Dynamics
Biophysics
Computational Biochemistry

Protein aggregation is a major challenge in the development of antibody-based therapeutics. Therapeutic antibodies are produced and stored in high concentrations and under fluctuating conditions unfavourable for their stability. Aggregation of these proteins in solution leads to serious consequences for patients, with the initiation of immune reactions, which have the potential to be fatal, and in the loss of clinical potency. The types of aggregates formed by antibodies, and the processes that lead to their propagation are poorly understood. By studying these molecules via computational approaches, we are able to simulate and probe their tendency to aggregate on experimentally comparable timescales.
By performing small numbers of coarse grained simulations of immunoglobulin frag- ments it is shown that specific regions of proteins are involved in self-self interactions, and these regions are targets for reducing the self-association of experimental molecules. Techniques developed here are integrated within a high throughput approach that is able to generate information on aggregation for a large number of candidate antibody structures.
The methodology was refined via development of a novel technique for coarse grained simulations of oligosaccharides. This method was initially tested on glycolipids, and then extended to glycoproteins. The primary outcome is a coarse grained model for a glyco- sylated antibody Fc fragment. The glycosylated Fc was then simulated, and compared to experimental data. Coarse grained simulations support the hypothesis that the protein be- comes more flexible in the absence of glycosylation.