Manufactured CeO2 nanomaterials (CeO2-MNMs) are used for a wide variety of applications including diesel fuel additives and chemical/mechanical planarization media. To test the effects of CeO2-MNM surface coating charge on to model organism Caenorhabditis elegans, we synthesized 4 nm CeO2 with cationic (DEAE-), anionic (CM-), and neutral (DEX) coatings. In L3 nematodes exposed for 24 hours, DEAE-CeO2 induced lethality at lower concentrations than CM- or DEX-CeO2. Feeding slightly decreased CeO2 toxicity, regardless of coating. In L2 nematodes exposed for 48 hours with feeding, DEAE-CeO2 caused lethality at the lower concentrations as compared to CM- and DEX-CeO2. Sublethal effects were measured by observing reproduction and oxidative/nitrosative protein damage. Low concentrations of DEAE-CeO2 induced similar reductions as CM- and DEX-CeO2 that were two orders of magnitude higher. Using immunochemical slot blots to explore oxidative/nitrosative stress, no treatments produced significant changes in protein carbonyl or 3-nitrotyrosine formation; however, the statistical power of our assay was low. All treatments caused large but not statistically significant increases in protein carbonyl levels. DEAE-CeO2 exposure caused a significant reduction in 4-hydroxy-2-nonenol levels. This research suggests that cationic coatings render CeO2 significantly more toxic to C. elegans than neutral or anionic coatings.

This thesis focuses on the role and historical development of strategies of experimental domestication in scientific knowledge production, with a particular focus on the function of the laboratory strains known as 'wild types' in the model organism systems of classical genetics, where they play the role of standing in for the 'natural' instance of the species so that variation may be measured. As part of establishing how lab wild types came to assume this role, I have situated them within a much longer historical trajectory that tracks how changes in the manner that European intellectual traditions conceptualised the domestic-wild divide were linked to the development of new forms of scientific domestication and knowledge production. These new developments required that existing domesticating practices be intensified, expanded and analogised in order to better control, capture and comprehend 'wild' nature. My first two chapters introduce the domestic-wild divide by discussing both contemporary and ancient interpretations of it. In my third and fourth chapter, I explore the roots of the knowledge regime of European scientific domestication. I highlight Francis Bacon's campaign to use knowledge of domesticating practices to restore human dominion, before showing how Linnaeus later re-conceptualised the natural economy as an autonomous order and original order, with domestication reinterpreted as an artful transformation of nature requiring human maintenance to prevent reversion to its wild 'natural state'. I identify this idea of the wild as original and the domestic as derivative and artificially maintained as the basis of the original wild type concept. In my fifth chapter, I discuss Darwin's attempt to unite the domestic and wild under common laws of variation and selection, including his argument that reversion was simply a product of a return to ancestral conditions of existence. I observe that Darwin's theory of variation was problematic for the effort to bring wild nature under controlled conditions for study, so in my sixth and seventh chapters discuss how this difficulty was resolved, first by experimental naturalists both before and after Darwin who utilised vivaria and microscopes to bring pieces of nature indoors, and then by Weismann and Galton's sequestration of heredity, which helped persuade scientists that domestication was not in itself a cause of germinal variation. In my eighth and ninth chapter, I detail how sequestration led the early Mendelians de Vries and Bateson to assume that wild types could be brought into the lab from nature and purified into true-breeding strains. I discuss their differing atomist and interactionist perspectives on wild type, with de Vries favouring 'elementary species' as units of nature, whereas Bateson held wild types and mutants to represent normal and abnormal forms of the species respectively. In my last chapter, I cover the replacement of Bateson's interactionist genetics by the reductionist genetics of the Morgan group and argue that this led to a disintegration of wild types into their component genes. I conclude with a discussion of what wild type strains in classical genetics were meant to be representative of, and end by establishing that whilst these strains may not wholly be representative of their species, they are nonetheless useful tools for scientific knowledge production.

This thesis examines literary texts that represent encounters with model organisms in ways that enact an interspecies ethics that turns the narrative of bodily relationality embedded within the model organism into a source of care, friendship, respect, and mourning. My project understands model organisms as material beings as well as semiotic and narrative entities; I suggest that the very ‘materiality’ of the model organism’s body is symbolic precisely because it is designed to refer to bodies other than its own. The model organism involves a double relationality between the categories of ‘animal’ and ‘human’ because it serves as a mediator between human nature and nature at large. This is not to say that that human biology is not part of ‘nature’ but rather that anthropocentric and human exceptionalist ideologies pervade discourses of human biology and thus the model organism provides a link to our biological and corporeal ‘selves’ in a way that maintains species divisions. The texts I analyze throughout this dissertation offer alternative ways of thinking about the model organism by exposing the multiple meanings and narratives that coexist within them both as representations and as living sentient beings. This project centers around two questions: How do cultural texts represent and negotiate disconnects between how model organisms signify within scientific discourses and their broader cultural identities? How does literature specifically engage with scientific knowledge in ways that both disrupt and affirm the status of the model organism as a scientific object? / Thesis / Doctor of Philosophy (PhD)

Cette thèse est dédiée aux développements méthodologiques et applications de la métabolomique par Résonance Magnétique Nucléaire (RMN) à très hauts champs. La première partie de ce manuscrit est dédiée à une présentation générale de la métabolomique par RMN. Nous décrivons ensuite les résultats obtenus concernant l’introduction d’une technique à dimensionnalité réduite pour la caractérisation des mélanges complexes, dénommée spectroscopie RMN par projections ciblées. La seconde partie de ce manuscrit décrit les résultats de trois études métabolomiques portant sur des populations humaines. La première analyse démontre que les échantillons de sérum collectés dans le cadre de la cohorte européenne prospective internationale EPIC sont appropriés pour une étude métabolomique. Les deux études suivantes recherchent une signature métabolique dans le sérum du cancer du sein métastatique et une signature plasmatique potentielle pour différentes pathologies hépatiques comme le carcinome hépatocellulaire. La troisième partie de cette thèse est dédiée à l’étude d’organismes modèles. La première étude caractérise les différences métaboliques systémiques entre quatre souches de rats couramment utilisées comme contrôles en génétique. Dans la seconde analyse, nous étudions les effets du vieillissement physiologique chez Caenorhabditis elegans (C. elegans), observons que le processus de restriction alimentaire tamponne les modifications métaboliques associées au vieillissement et que des perturbations du métabolisme de la phosphocholine corrèlent avec l’espérance de vie. La troisième étude caractérise des modifications métaboliques importantes chez un mutant de C. elegans, pour le gène ahr-1, suggérant un rôle dans le développement et le vieillissement. Enfin, nous étudions les effets au niveau métabolique de l’interaction entre la protéine endogène E4F1 et la protéine virale HBx dans des cellules hépatiques infectées par le virus de l’hépatite B. / This thesis is dedicated to developments and applications of metabolomics, exploiting high field NMR spectroscopy. The first part is dedicated to a general presentation of metabolomics. We also report results about the introduction of reduced dimensionality techniques for the characterization of complex mixtures, coined targeted projection NMR spectroscopy. The second part of this manuscript reports results about three different metabolomic studies carried out in human populations. The first analysis demonstrates the suitability for metabolomics of serum samples collected in the framework of the European Prospective Investigation into Cancer and Nutrition (EPIC) study. The second study investigates a serum metabolic signature of metastatic breast cancer. The last analysis establishes potential plasma metabolic signatures for different liver pathologies, like hepatocellular carcinoma. The third part of this thesis is dedicated to the characterization of various model organisms. The first study presents a characterization of plasma and urine metabolic differences between four rat strains commonly used as controls in genetic studies. In the second study, we investigate the effects of physiological aging in Caenorhabditis elegans (C. elegans) and observe that dietary restriction buffers metabolic changes associated with aging. We further identify that perturbations in phosphocholine metabolism correlate with life expectancy. The third analysis of this part characterizes the ahr-1 C. elegans mutant, showing strong metabolic changes in ahr-1 mutants, which suggest an involvement in development and aging processes. We finally investigate in the last study the effects at the metabolic level of the interaction between an endogenous protein E4F1 and a viral protein HBx in liver cells infected by hepatitis B virus.

Zebrafish, a novel vertebrate model organism, has a high nucleotide sequence homology with human genes. Its transparent and fast developing embryo allows the analysis of physiological and anatomical characteristics, many of which are similar to those of mammals. Although the prolific nature of zebrafish can facilitate genetic studies, linking genes and behaviour is difficult because behaviour is not well investigated in zebrafish. The aim of this project is to develop robust behavioural tests that can quantify shoaling with conspecifics and fear responses to natural predators. Eight conditions using different computer-animated stimuli were used to induce behavioural responses. The results demonstrate that shoaling behaviours and fear responses can be successfully induced. More importantly, the behaviours caused by the computer-animated images confirm previous research findings using natural conspecifics and predators. Thus, computer-animated images will help standardize behavioural tests in zebrafish and will lead the way to more sophisticated and better controlled experiments.

Zebrafish, a novel vertebrate model organism, has a high nucleotide sequence homology with human genes. Its transparent and fast developing embryo allows the analysis of physiological and anatomical characteristics, many of which are similar to those of mammals. Although the prolific nature of zebrafish can facilitate genetic studies, linking genes and behaviour is difficult because behaviour is not well investigated in zebrafish. The aim of this project is to develop robust behavioural tests that can quantify shoaling with conspecifics and fear responses to natural predators. Eight conditions using different computer-animated stimuli were used to induce behavioural responses. The results demonstrate that shoaling behaviours and fear responses can be successfully induced. More importantly, the behaviours caused by the computer-animated images confirm previous research findings using natural conspecifics and predators. Thus, computer-animated images will help standardize behavioural tests in zebrafish and will lead the way to more sophisticated and better controlled experiments.

Gadoliumbasierte Kontrastmittel werden in der Magnetresonanztomographie verwendet und gelangen nach der Exkretion durch behandelte Patienten in Oberflächengewässer, da sie von Klärwerken nur unzureichend entfernt werden. Das Verhalten der Kontrastmittel in der Umwelt und deren Wechselwirkung mit Organismen wurde in dieser Arbeit aufgrund der Toxizität des freien Gd-Ions und der damit verbundenen möglichen Gefahren, wie der Anreicherung in der menschlichen Nahrungskette, näher untersucht. Die bildgebenden elementanalytischen Methoden Laserablation mit induktiv gekoppelter Plasmamassenspektrometrie (LA-ICP-MS) und Röntgenfluoreszenzanalyse mit Synchrotronstrahlung (SRXRF) wurden genutzt, um verschiedene biologische Systeme hinsichtlich ihrer Aufnahme, Verteilung und Abgabe von Gd-basierten Kontrastmitteln zu untersuchen. Zuvor wurden beide Methoden für diese Anwendung analytisch charakterisiert und verglichen. Die Nachweisgrenzen von Gadolinium wurden mittels LA-ICP-MS (0.78 pg) und SRXRF (89 pg) unter jeweils optimierten Bedingungen durch die Kalibrierung über Rückstände eingetrockneter Elementstandardtropfen bestimmt. Anhand von Fadenalgen konnte die Aufnahme und Abgabe der Gd-basierten Kontrastmittel gezeigt werden. Die Abhängigkeit von der Konzentration des Kontrastmittels in der Expositionslösung und die Unabhängigkeit der zeitlichen Aufnahme innerhalb eines Zeitraums von 1-7 Tagen wurden an Wasserlinsen studiert. Gadolinium konnte in einem Kresseblatt quantifiziert werden. Die Verifizierung der LA-ICP-MS-Ergebnisse erfolgte mit der SRXRF und der ICP-MS nach Aufschluss. Auch die Aufnahme und Abgabe von Gd in Wasserflöhen wurde beobachtet. Die Lokalisierung des Gds wurde mittels 3D µ-Computertomographie durch den Vergleich mit einem unbelasteten Wasserfloh aufgeklärt. In allen Untersuchungen wurde Gadolinium in den exponierten Modellorganismen nachgewiesen, woraus geschlussfolgert werden kann, dass die Kontrastmittel aus der Umgebung aufgenommen werden. / Gadolinium based contrast agents are used for magnetic resonance imaging. After their excretion by medicated patients they reach surface water passing waste water treat-ment plants where they are not removed sufficiently. The behavior of the contrast agents in the environment and the interaction with organisms was investigated in this work due to the toxicity of the free Gd3+ ion and the associated risks, such as accumulation in the human food chain. In this work, the two elemental analytical imaging methods laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and synchrotron radiation X-ray fluorescence analysis (SRXRF) have been used to investigate the uptake, distribution, and excretion of Gd-based contrast agents by various biological systems. Both methods were analytically characterized and compared for this application. The detection limits of gadolinium were determined under optimized conditions by LA-ICP-MS and SRXRF. With calibration by remains of dried elemental standard droplets detection limits of 0.78 pg absolute amount of gadolinium (LA-ICP-MS), respectively 89 pg (SRXRF) were reached. Based on filamentous algae as water plants the uptake and the excretion of Gd-based contrast agents were revealed. The dependence on concentration of the contrast agent in the exposition solution and the independence of temporal uptake within one to seven days were studied for duckweed. By LA-ICP-MS gadolinium was quantified in a leaf of cress plant. The verification of the results was performed by SRXRF and ICP-MS after digestion. Furthermore, the uptake and distribution of Gd-based contrast agents in higher organisms (water flea) were observed. The exact location of gadolinium was resolved by three-dimensional μ-computed tomography by the comparison of an exposed with a Gd-free water flea. In all studies, gadolinium was detected in the investigated exposed model organisms. It can be concluded that the contrast agents were taken from the environment.

This work expands the knowledge on phospholipid metabolism in the kinetoplastid parasites: T. brucei, T. cruzi, Leishmania spp. that cause neglected tropical diseases and the related non-human pathogenic Crithidia fasiculata. As a close relative of parasitic kinetoplasts, specifically Leishmania, it is hypothesised that Crithidia fasiculata possesses a similar lipid biosynthetic capability and therefore represent an attractive model organism. Database mining the Crithidia genome revealed the ability to biosynthesise all of the main phospholipid species. Utilising various lipidomic techniques, a high level of an ω-6 18:3 fatty acid was observed, alongside an uncommon Δ19:0 fatty acid that was later identified to be exclusive attributed to PE species. Sphingolipid metabolism was shown to resemble that of Leishmania and T. cruzi, given the exclusive production of inositol-phosphoceramide species and no sphingomyelin species being observed. Using labelled precursors, Crithidia were seen to uptake and incorporate extracellular inositol into both phosphatidylinositol and inositol-phosphoceramide species. Crithidia were also shown to utilise both the Kennedy pathway and methylation of phosphatidylethanolamine to form phosphatidylcholine. The phospholipidome of T. cruzi revealed several phosphatidylserine species for the first time, suggesting a functional phosphatidylserine synthase. Current knowledge of T.cruzi sphingolipid biosynthesis was also confirmed as only inositol xxxi phosphoceramide species were observed. The identification and subsequent characterisation of novel phosphonolipid species are reported for the first time. Utilising lipidomic methodologies and labelled precursors, the relative contribution of the intracellular inositol pools within bloodstream and procyclic T. brucei towards PI biosynthesis was examined. This highlighted that the synthesis/turnover rates for specific phosphatidylinositol and inositol-phosphoceramide species are unequal. Efforts to optimise media conditions highlighted that under reduced levels of serum/glucose/inositol, bloodstream T. brucei unexpectedly adjusts its inositol metabolism. The procyclic parasite exemplifies this fact, as under inositol/glucose deficient media conditions they appear to have adapted to utilising glucogenesis and inositol de-novo synthesis. This work highlights that these parasites are rapidly dividing, their unique features of lipid metabolism may be exploitable for drug discovery purposes.

A major goal of evolutionary developmental biology is to explore mechanisms and events underlying evolution of the myriad body plan morphologies expressed both genetically and phenotypically within the animal kingdom. Arthropods exhibit an astounding array of morphological diversity both within and between representative sub-phyla, thus providing an ideal phylum through which to address questions of body plan innovation and diversification. Major arthropod groups are recognised and defined by the distinct form and number of articulated appendages present along the antero-posterior axis of their segmented bodies. A great deal is known about the developmental genetics of limb development in the model insect Drosophila melanogaster, added to which, much comparative gene expression data and a growing body of functional genetic data is emerging for other arthropod species. Arthropod limb primordia are consistently marked by expression of the homeobox gene Distal-less (Dll), and the focus of this thesis is to compare signalling mediated by early Dll regulatory genes activity along antero-posterior and dorso-ventral embryonic axes during limb specification in Drosophila, with the activity of their orthologs in the widely disparate chelicerate, the spider mite Tetranychus urticae - interpreting new data with that available for other arthropods. Having made a detailed study of spider mite embryonic (and post-embryonic) development, to provide a basis for understanding mRNA transcription and protein activity patterns, I confirmed typical expression of Tetranychus Dll in prosomal limb primordia. I obtained limited results for the candidate antero-posterior positioning genes wingless and engrailed, although one of the two engrailed paralogs I identified is reportedly expressed in posterior segmental compartments, consistent with possible conservation of Engrailed-Wingless interactions in metameric patterning and positive regulation of Dll in arthropod limb specification. In Drosophila, wingless-dependent Dll transcription is restricted along the dorso-ventral axis by dorsal Dpp-mediated and ventral EGFR-mediated signalling gradients. Based on data from Tetranychus and other arthropods, neither dorsal nor ventral signalling regimes appear conserved outside the Drosophila system. Dll suppression in fly abdominal segments occurs due to powerful Hox (Ubx/AbdA) repression of the early Dll cis-regulatory element; this is discussed in relation to the independently evolved limbless chelicerate opisthosoma, informed by hypothetical scenarios of cis (regulatory DNA) and trans (coding sequence) evolution. Given practical difficulties and limitations encountered while working with spider mites, I offer a final assessment of the place of Tetranychus urticae as a non-model, and yet still valuable chelicerate species to consider carrying into the exciting future of evolutionary developmental biology.

No description available.