Cette étude s’inscrit dans le cadre d’un problème biologique et son objectif est de comprendre les mécanismes d’assemblage des protéines. L’assemblage d’une protéine en oligomère est particulièrement important car il est impliqué dans de nombreuses pathologies allant de l’infection bactérienne aux maladies de type Alzheimer ou même des cancers. L’assemblage protéique est un mécanisme de combinaison de deux ou plusieurs chaînes protéiques, il est aussi par ailleurs souvent utilisé par les organismes vivants pour déclencher une activité biologique. La sous unité B de la toxine du choléra(CtxB5), qui appartient à la famille des toxines AB5, est étudiée comme modèle principal de l’assemblage. Des résultats expérimentaux ont fourni des informations sur l’assemblage de la toxine mettant en avant l’implication de certains acides aminés. La première question que j’ai abordée pendant ma thèse était de comprendre leur rôle et de voir si les approches réseaux étaient pertinentes pour y répondre. J’ai pu montrer en utilisant des mutations d’acides aminés que ces derniers s’influençaient entre eux suivant des mécanismes en cascade ou de « Peer to Peer » afin de coordonner les étapes de l’assemblage (les chapitres 4, 5 et 6). La structure et la fonction des protéines sont définies par des séquences d’acides aminés qui varient naturellement en raison de mutation génétique. J’ai donc décidé d’élargir ce champ d’investigation pour voir si le mécanisme en cascade était généralisable comme moyen de perturber une structure de protéine par le biais d’une mutation. Ici il s’agit de comprendre les changements de structure liés à des mutations et pouvant menés à des maladies. J’ai tout d’abord étudié des jeux de données pour connaître les caractéristiques réseaux de protéines saines (chapitre 7, 8 et 9), avant de regarder l’effet de la mutation systématique de chacun des acides aminés de CtxB5 sur sa structure globale (chapitre 10 et 11). Les mutations peuvent engendrer des changements de structure modérés ou très grand autour de l’acide aminé muté ou à des distances très éloignées. Ces résultats sont consistants avec tous les effets connus de mutation : robustesse (maintien de la fonction), évolution ou adaptation (émergence d’une nouvelle fonction) et fragilité (pathologies). Les résultats montrent aussi une faible corrélation entre le nombre de contacts d’un acide aminé et la quantité de changement structuraux induit par sa mutation. Il n’est donc pas simple d’anticiper l’effet d’une mutation : Le dernier chapitre de ma thèse aborde ce problème (chapitre 12). / The aim of this study is to understand protein assembly mechanisms. The assembly of a protein in an oligomer is particularly important because it is involved in many pathologies going from bacterial infection, Alzheimer like diseases or even some cancers. Protein assembly is the combination of two or more protein chains to induce a biological activity. The B subunit of the cholera toxin pentamer (CtxB5), which belongs to the family of AB5 toxins, is studied as the main model of assembly. Experimental results have provided information on the assembly of the toxin highlighting the involvement of certain amino acids. The first problem addressed in my thesis is to understand their role and see if network approaches are relevant to such investigation. I was able to show using amino acid mutations, that amino acids influence each other by cascade or "peer to peer" mechanisms in order to coordinate the various steps of the assembly (Chapters 4, 5 and 6). The structure and function of the proteins are defined by amino acid sequences which naturally vary due to genetic mutation. So I decided to expand this field of investigation to see if the cascade mechanism was generalized as a mean of disrupting a protein structure. Here it is to understand how a protein loses its function by way of a significant change of structure upon mutation. First, I studied dataset to know the characteristics of healthy protein networks (Chapter 7, 8 and 9), and after I looked at the effects of the systematic mutation of each amino acid of CtxB5 on its overall structure (Chapter 10 and 11). Mutations led from moderate to very large structural changes around the mutated amino acid or at long distances. These results are consistent with known effects of mutation: robustness (maintenance function), evolution or adaptation (emergence of a new feature) and fragility (pathologies). The results also show a weak correlation between the number of amino acid contacts of the mutated amino acid and the amount of structural change induced by its mutation. It is therefore not easy to anticipate the effect of a mutation: The last chapter of my thesis addresses this problem (Chapter 12).

Les virus sont connus pour infecter toutes les classes d’organismes vivants sur Terre, qu’elles soient végétales ou animales. Les virions consistent en un génome d'acide nucléique protégé par une enveloppe protéique unique ou multicouche appelée capside et, dans certains cas, par une enveloppe de lipides. La capside virale est généralement composée de centaines ou de milliers de protéines formant des structures ordonnées. La moitié des virus connus présentent une symétrie icosaédrique, les autres étant hélicoïdaux, prolats ou de structure irrégulière complexe. Récemment, les particules virales ont attiré une attention croissante en raison de leur structure extrêmement régulière et de leur utilisation potentielle pour la fabrication de nanostructures ayant diverses fonctions. Par conséquent, la compréhension des mécanismes d'assemblage sous-jacents à la production de particules virales est non seulement utile au développement d'inhibiteurs à des fins thérapeutiques, mais elle devrait également ouvrir de nouvelles voies pour l'auto-assemblage de matériaux supramoléculaires complexes. À ce jour, de nombreuses études expérimentales et théoriques sur l'assemblage de virus ont été effectuées. Des recherches expérimentales ont permis d'obtenir de nombreuses informations sur l'assemblage du virus, y compris les conditions appropriées requises pour l'assemblage et les voies cinétiques. En combinant ces informations et méthodes théoriques, une première compréhension du mécanisme d'assemblage des virus a été élaborée. Cependant, les informations provenant uniquement d'expériences ne peuvent donner une image complète, en particulier à l'échelle microscopique. Par conséquent, dans cette thèse, nous avons utilisé des simulations informatiques, y compris des techniques de Monte Carlo et de la dynamique moléculaire, pour sonder l’assemblage du virus, dans l’espoir de mieux comprendre les mécanismes moléculaires en jeu. / Viruses are known for infecting all classes of living organisms on Earth, whether vegetal or animal. Virions consist of a nucleic acid genome protected by a single or multilayered protein shell called capsid, and in some cases by an envelope of lipids. The viral capsid is generally made of hundreds or thousands of proteins forming ordered structures. Half of all known viruses exhibit an icosahedral symmetry, the rest being helical, prolate or having a complex irregular structure. Recently, viral particles have attracted an increasing attention due to their extremely regular structure and their potential use for fabricating nanostructures with various functions. Therefore, understanding the assembly mechanisms underlying the production of viral particles is not only helpful to the development of inhibitors for therapeutic purpose, but it should also open new routes for the self-assembly of complex supramolecular materials. To date, numerous experimental and theoretical investigations on virus assembly have been performed. Through experimental investigations, a lot of information have been obtained on virus assembly, including the proper conditions required for the assembly and the kinetic pathways. Combining those information and theoretical methods, an initial understanding of the assembly mechanism of viruses has been worked out. However, information coming purely from experiments cannot give the whole picture, in particular at a microscopic scale. Therefore, in this thesis, we employed computer simulations, including Monte Carlo and molecular dynamics techniques, to probe the assembly of virus, with the expectation to gain new insights into the molecular mechanisms at play.

This interdisciplinary dissertation, The Rhetoric of Wolves, attempts to answer a simple, yet broad question: What do we talk about when we talk about wolves? While even the “we” here is contentious, as there are many perspectives and positions through which the wolf is figured, there are also many kinds of wolves, but no “real” wolf. That is, this dissertation takes seriously the contention that has recently arisen in the environmental humanities and animal studies through the late work of Jacques Derrida and others that figurations of “the animal” matter, not only for multi-species relations and coexistence, but for how the subject and polity are constructed and normalized. As these discourses put “the animal” into question, that is, how the animal functions as a discursive resource in socio-political issues, so too does this dissertation question how “the wolf” functions discursively in contemporary socio-political issues in North America. To address these questions, this dissertation utilizes a Foucaultian-inspired genealogical analysis of the discourse around “the wolf” understand how rhetoric about wolves coalesces into what I call “rhetorical assemblages” that vie to become regimes of truth that are used to attempt to settle the identity of the wolf and human-“animal” relations through the productive capacity of various power/knowledges that are historically and materially grounded. To do so, this dissertation examines and analyzes the rhetoric of a series of case studies in North America where figurations of wolves produce “the wolf” variously as man-hunting machines, outlaws that disrupt the natural order, illegal immigrants threatening family and tradition, and always already potential terrorists who must be productively managed through a biopolitics that attempts to make good the expectations of the dominant neoliberal frame of contemporary social and political life. / Graduate / 2023-08-15

Over 22,000 sherds of pottery were recovered during the excavation of the small islet of Eilean Dòmhnuill in North Uist in the late 1980s. Analysis of the assemblage has demonstrated that all of the main vessel forms and decorative motifs recognised at the site were already in place when settlement began in the earlier 4th millennium BC and continued to be deposited at the site until its abandonment over 800 years later. Statistically significant stylistic variation is limited to slow drifts in the relative proportions of certain rim forms. Across the Outer Hebrides, decorative elaboration and the presence of large numbers of distinctive vessel forms would appear to mark out certain assemblages seemingly associated with communal gathering and feasting events at key locales within which a distinctive Hebridean Neolithic identity was forged. Throughout, this study takes a relational approach to the issue of variation in material culture, viewing all archaeological entities as dynamic assemblages that themselves form attributes of higher-level assemblages. It is argued that the various constraints and affordances that arise within such assemblages constitute significant structuring principles that give rise to commonly held expectations and dispositions, resulting in the kind of constrained temporal and spatial variation that we observe in the archaeological record and which in turn gives rise to the concept of the archaeological culture. / Faculty of Life Sciences at the University of Bradford / Erratum: Vol. 1: 196 and Vol. II: xii and 383 It should be noted that the Unstan-type bowl recorded as being from Loch Mor is actually from Loch Arnish (Chris Murray pers. comm.). The appendices including 'An Doirlinn Report and Illustrations' and 'St Kilda Report and Illustrations' are not available online due to copyright.

This thesis explores different ways of relating to forests, and thus also different types of forestry. Starting with the Swedish forest industry one which is characterized by the planting of forests at the expense of natural regeneration, thus making Sweden the fifth country in the world in terms of planted area the study then examines different forests. This study is conducted with qualitative methods and by “following the seed” looks at various actors’ interests and potential flaws in the venture of planting forests. Different possibilities of doing forestry are explored in the thesis through letting modern forestry meet local forest-owners as well as a seed-collecting practice in central Sweden.  These processes are explored by understanding the forest as an assemblage of historical decisions, species and human interests, tracing relations and powers within and beyond forestsfrom a more-than-human perspective. Forestry emerges as an attempt at domestication of the forest and the thesis explores how it goes wild, as well as the meeting of modern industrialism and science with other world views, values and practices. This allows for an alternative understanding of forests, forestry beyond industrialism and modernity, and what sort of futures we might have living together with forests.

<p> The Potterdoal volcanogenic massive sulphide deposit is hosted by a tholeiitic/komatiitic succession located in northern Munro Township, Ontario. An integrated surface and drill core study of this property was undertaken to document the three dimensional structure and stratigraphy of the deposit. Petrography focused on mineralogical changes associated with the hydrothermal alteration within specific units. Several geochemical methods were used to determine the effects of hydrothemal alteration (as quantified by elemental mobility) as well as source magma affinities and tectonic setting. Based on this information, a model for ore genesis was developed. </p> <p> The Potterdoal deposit is hosted by volcanic rock of an iron tholeiite affinity, emplaced within an ocean floor rifting environment. The chemistry of the tholeiites shows similarities to that of large deposits like Kidd Creek, but lacks the felsic component of bimodal volcanism. It is suggested that felsic volcanics are absent because the local crust did not achieve sufficient thickness to allow partial melting of lower crustal material. </p> <p> The deposit consists of a stockwork zone overlain by an extensive massive sulphide lens which lies along a scarp structure defmed in the paleosurface. Stockwork mineralization is narrowly confined to conduits within a fault breccia in the footwall Ore Flow. gabbro, and widens into an overlying tectonic breccia. Sulphide paragenesis appears to be controlled by the thermal solubilities ofthe sulphide minerals, and consists of pyrite, sphalerite, pyrrhotite and chalcopyrite in both stockworks and the massive sulphide lens. The lens occurs at the top of the tectonic breccia near the paleo-seawater interface, and formed by direct replacement of the tectonic breccia. The lens locally exhibits ore grade base metal values (i.e. combined Cu and Zn content of at least 3% ), and shows an upward and outward gradation from chalcopyrite to sphalerite-dominated ore. These features suggest that exhalation of the hydrothermal system was focused into local vent sites. </p> <p> Mass change associated with the hydrothermal alteration envelopes surrounding Ore Flow fault breccia conduits involve loss of Si, Ca, Na and Sr, and gain of Fe, Mg, K, Cu and Zn. These changes are attributed to fluid-rock reactions which are consistent with hydrothermal alteration associated with other VMS deposits, The genetic model suggested for the Potterdoal deposit involves a hydrothermal system driven by heat from the intrusion ofthe Munro-Warden Sill at a high stratigraphic level. The relatively small size of the deposit is probably due to the rapid cooling of the sill, which shortened the life-span of the hydrothermal system. The primary source of metals was the upper portion of the Munro-Warden Sill, as indicated by the high degree of pervasive hydrothermal alteration of this part of the gabbro. </p> <p> Drill core information has also revealed the importance of the Buster Fault in the construction of the currently exposed Potterdoal stratigraphy. Thrusting subparallel to bedding along the Buster Fault during the Kenoran compressional event(~2.6 Ga) was responsible for the local repetition of tholeiitic flows, and has effectively removed the deep footwall rocks originally associated with the Potterdoal mineralization. </p> / Thesis / Master of Science (MSc)

Fibre plants favour different growth conditions and require different levels of husbandry. However, the fibres share some physical and material properties, which make them difficult to distinguish in the archaeological record. This thesis evaluates the effectiveness of methods for characterising bast fibres including; fibre chemical analysis, mechanical testing and fibre morphology, to propose that longitudinal microfibrillar angle (MFA) and cross-sectional circularity (Ct) used in a two-step procedure to analyse selected modern fibres of nettle (Urtica dioica L.), flax (Linum usitatissimum L.) and hemp (Cannabis sativa L.) could offer an alternative approach. The reliability of MFA and Ct, as diagnostic features, was evaluated under a temperature accelerated degradation 48week trial with eight fibre types from three deposition soils Post deposition, surviving fibres were subjected to evaluation of changes in MFA and Ct. An additional check on the diagnostic efficacy was conducted within a blind-test protocol. Finally, the research programme employs MFA and Ct in the diagnosis of a range of archaeological textile fibres from museum collections and fibres from the Kasr el Yahud mass burial. The thesis includes recommendations to address future post thesis research programmes.

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