RNA Localization and Translational Regulation on the Endoplasmic Reticulum

mRNA localization is emerging as a critical cellular mechanism for the spatiotemporal regulation of protein expression and serves important roles in oogenesis, embryogenesis, cell fate specification, and synapse formation. Signal sequence-encoding mRNAs are localized to the endoplasmic reticulum (ER) membrane by either of two mechanisms, a canonical mechanism of translation on ER-bound ribosomes (signal recognition particle pathway), or a poorly understood direct ER anchoring mechanism. In this study, we identify that the ER integral membrane proteins function as RNA-binding proteins and play important roles in the direct mRNA anchoring to the ER. We report that one of the ER integral membrane RNA-binding protein, AEG-1 (astrocyte elevated gene-1), functions in the direct ER anchoring and translational regulation of mRNAs encoding endomembrane transmembrane proteins. HITS-CLIP and PAR-CLIP analyses of the AEG-1 mRNA interactome of human hepatocellular carcinoma cells revealed a high enrichment for mRNAs encoding endomembrane organelle proteins, most notably encoding transmembrane proteins. AEG-1 binding sites were highly enriched in the coding sequence and displayed a signature cluster enrichment downstream of encoded transmembrane domains. In overexpression and knockdown models, AEG-1 expression markedly regulates translational efficiency and protein functions of two of its bound transcripts, MDR1 and NPC1. This study reveals a molecular mechanism for the selective localization of mRNAs to the ER and identifies a novel post-transcriptional gene regulation function for AEG-1 in membrane protein expression.

Kinase C substrates and synaptic plasticity in Aplysia

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Contribution des réserves calciques présynaptiques et gliales dans la modulation de la transmission synaptique à la jonction neuromusculaire de la grenouille Rana pipiens

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Beyond Black and White: The grisaille exterior of the Netherlandish triptych

This thesis is a study of fifteenth- to mid sixteenth-century Netherlandish triptych exteriors, focusing on the so-called ‘grisaille’ technique. During this period, altarpieces produced in the Low Countries were typically constructed in a tripartite format with folding wings. This arrangement created the opportunity for pictorial representations on both sides of the hinged panels. Painters emphasized the distinction between the triptych’s two faces by executing the exteriors in a strikingly more subdued palette than the interiors. Particular iconographic subject matter was favoured for grisailles, which often depict the Annunciation or saints that reflect the triptych’s patronage or intended location. Jan van Eyck was notable for his emphasis on imitating stone statuary and created three important grisailles, one of which would influence triptych exteriors for years to come. Hieronymus Bosch, an artist working at the turn of the sixteenth century, also brought innovation to his grisailles, further expanding the potential of these reduced-palette paintings. This thesis examines the creative process involved in the production of grisailles and compares the underdrawings of triptych exteriors to those of the corresponding polychromatic interiors. In this study, grisailles are situated in their context as part of multifaceted artworks as well as within the broader church environment. New infrared reflectograms were generated using Queen’s OSIRIS infrared camera to document works in Belgium and the Netherlands. While some aspects of underdrawings could indicate that the figure was meant to imitate statuary, this distinction was not directly linked to triptych exteriors and was related instead to efforts at a trompe-l’oeil effect. Such attempts at mimicry can also be found on triptych interiors. Through a close examination of the underdrawing stage of these paintings it appears that this part of the creative process was not distinguished in any significant way from the underdrawings of triptych interiors.

Sweat Lodges in Iron Age Iberian Peninsula: New Data, Typologies and Interpretations

Three questions on the study of NO Iberian Peninsula sweat lodges are posed. First, the new sauna of Monte Ornedo (Cantabria), the review of the one of Armea (Ourense), and the Cantabrian pedra formosa type are discussed. Second, the known types of sweat lodges are reconsidered underlining the differences between the Cantabrian and the Douro - Minho groups as these differences contribute to a better assessment of the saunas located out of those territories, such as those of Monte Ornedo or Ulaca. Third, a richer record demands a more specific terminology, a larger use of archaeometric analysis and the application of landscape archaeology or art history methodologies. In this way the range of interpretation of the sweat lodges is opened, as an example an essay is proposed that digs on some already known proposals and suggests that the saunas are material metaphors of wombs whose rationale derives from ideologies and ritual practices of Indo-European tradition.

Finding the idea of home

La notion de chez-soi est porteuse d’un imaginaire foisonnant et génère un grand intérêt dans notre culture et société. Bien qu’elle soit une considération importante pour la plupart d’entre nous, l’architecte occupe une position privilégiée qui lui permette d’agir sur le chez-soi de manière significative et tangible. La présente recherche explore le concept du chez-soi tel qu’étudié par les architectes et non-architectes de manière à comprendre son impact sur la création du lieu et sur la construction des environnements domestiques en Amérique du nord. Un regard porté sur les connotations entre espace et lieu, à travers la temporalité, les comportements et les perspectives sociales, supporte l’épistémologie du chez-soi comme un élément important des théories et pratiques de design contemporain. Le démantèlement hypothétique d’un espace en ses composantes suppose que les dispositifs architecturaux peuvent être modelés de manière à ce qu’ils opèrent un transfert depuis la maison, en tant qu’élément physique, vers le domaine psychologique du chez-soi. Afin d’élargir la maniabilité des éléments constitutifs du bâtiment et de son environnement, six thèmes sont appliqués à trois champs de données. Les six thèmes, qui incluent l’entre-deux, la limite, la voie, le nœud, le détail et la représentation, illustrent des moments architecturaux déterminants, potentiellement présents à l’intérieur et à l’extérieur du projet domestique et qui transforment les comportements physiques et psychiques. Depuis la pratique normalisée du logement social et abordable au Canada, une analyse de photographies de maisons abordables existantes, du discours critique sur cette typologie et de projets de recherche-création conduits par des étudiants en architecture, révèle le caractère opérationnel de la notion de chez-soi et consolide les valeurs de communauté et de frontière. L’objectif premier de la recherche est d’avancer la production de connaissances en architecture par l’exploration de la notion de chez­soi dans l’enseignement, la recherche et le design. L’approche fonctionnaliste vis-à-vis le < penser > en design, place l’usager au centre de l’environnement domestique, soutient la proposition que le chez­soi donne sens et utilité au logement, et renforce la responsabilité éthique de l’architecte à faire de cette notion une partie intégrante de la réalité quotidienne.

Habitudes problématiques de jeux de hasard et d’argent à l’adolescence: une analyse axée sur la perspective de l’acteur

Les approches visant à conceptualiser les habitudes problématiques de jeux de hasard et d’argent (JHA) à l’adolescence se distinguent sur deux aspects. Premièrement, par la nature des variables impliquées dans la conceptualisation du phénomène; la plupart des approches intègrent principalement des variables de nature individuelle dans leur modélisation alors que les variables de nature sociales sont encore peu prises en compte. Le deuxième aspect concerne la distinction entre déterminisme et interactionnisme : plusieurs approches semblent s’inscrire dans un courant déterministe et peu d’entre elles s’avèrent considérer l’individu comme un acteur social dynamique et en interaction avec son environnement. Or, il est essentiel d’examiner le sens que revêtent les comportements de JHA du point de vue des acteurs et au regard du contexte social dans lequel ils évoluent afin de mieux comprendre comment ils s’inscrivent dans leur réalité. La théorie générale de la rationalité (TGR), de Raymond Boudon, offre cette possibilité. Cette étude qualitative vise donc à comprendre les rationalités sous-jacentes aux comportements de JHA d’adolescents considérés comme manifestant des habitudes problématiques sur ce plan? Cet objectif général repose sur quatre objectifs spécifiques : 1) comprendre leurs premières expériences de JHA ainsi que leur évolution, 2) situer les expériences de JHA à l’intérieur de leur contexte (contexte social de jeu, partenaires de jeu, perception de l’entourage, etc.), 3) décrire les bénéfices et les conséquences négatives liés aux JHA et 4) décrire leur perception quant au degré de sévérité de leurs habitudes de JHA. La thèse s’appuie sur une analyse secondaire de données collectées dans le cadre d’un projet de recherche pancanadien dont l’objectif était le développement et la validation de l’Inventaire canadien des jeux de hasard et d’argent chez les adolescents (Tremblay et al., 2010). Les données utilisées portent sur l’expérience des adolescents ayant des habitudes problématiques de JHA. Elles ont été récoltées dans le cadre d’entrevues semi-structurées réalisées auprès de 31 adolescents présentant des habitudes problématiques de JHA en traitement pour leur consommation de substances psychoactives (SPA). L’analyse des propos des adolescents révèle que les bénéfices associés aux premières expériences de JHA et à leur exacerbation sont de nature matérielle, émotive et sociale. Par ailleurs, les contextes physiques et sociaux dans lesquels s’actualisent les comportements de JHA sont généralement les mêmes que ceux dans lesquelles se déroule l’usage de SPA. À cet effet, trois types de relations entre usage de SPA et habitudes de JHA ressortent du discours des adolescents: circulaire (les deux activités s’alimentent mutuellement), hiérarchique (l’une prime sur l’autre) et tripartite (les deux activités sont financées par des activités externes, souvent reliées à la délinquance). Les contextes dans lesquels s’opérationnalisent ces relations contribuent à leur renforcement, mais ont également le potentiel d’en favoriser l’affaiblissement et l’extinction. Les résultats obtenus révèlent que les comportements de JHA des adolescents s’inscrivent à l’intérieur de rationalité de nature instrumentale, cognitive et axiologique et que ces rationalités modulent leur perception du degré de sévérité de leurs habitudes de JHA. À cet effet, la théorie générale de la rationalité permet un éclairage nouveau afin de mieux comprendre comment les habitudes de JHA s’inscrivent dans la réalité des adolescents et pourquoi une proportion importante d’entre eux ne perçoit pas ces dernières comme problématiques.

Microtubule attachment and regulation mechanisms of the budding yeast kinetochore

Thesis (Master's)--University of Washington, 2016-08

The Genesis Of The Mycenaean Citadel: A Philosophical Quest For The Origins Of The Architectural Forms

This thesis deals with the origins of the architectural forms as expressed in the Homeric Mycenaean citadel. The Genesis of the Mycenaean Citadel is a philosophical quest which reveals the poetic dimension of the Mycenaean architecture. The Introduction deals with general theories on the subject of space, which converge into one, forming the spinal idea of the thesis. The ‘process of individuation’, the process by which a person becomes ‘in-dividual’ that is a separate, indivisible unity or ‘whole’, is a process of transformation and renewal which at collective level takes place within the citadel. This is built on the archetype which expresses both the nature of the soul as a microcosm and of the divinely ordered Cosmos. The confrontation of the rational ‘ego’ with the unconscious is the process which brings us to the ‘self’, that organising center of the human psyche which is symbolised through the centre of the citadel. . Chapter I refers to ‘the Archetype of the Mycenaean citadel’. The Mycenaean citadel, which is built on a certain pattern of placement and orientation in relation to landscape formations, reproduces images which belong to the category of the ‘archetypal mother’. On the other hand, its adjustment to a central point with ‘high’ significance, recalls the archetypal image of Shiva-Shakti. The citadel realises the concept of a Kantian ‘One-all embracing space’; it is a cosmogonic symbol but also a philosophical one. Chapter II examines the column in its dual meaning, which is expressed in one structure; column and capital unite within their symbolism the conscious and unconscious contents of the human psyche and express the archetype of wholeness and goal of the individuation process. 33 Chapter III is a philosophical research into the ‘symbolism of the triangle’, the sacred Pythagorean symbol which expresses certain cosmological beliefs about the relation between human nature and the divinely ordered Cosmos. The triangular slab over the Lion Gate is a representation of the Dionysiac ‘palingenesia’, that is the continuity of One life, which was central to the Mycenaean religion. Chapter IV deals with the tripartite ‘megaron’. The circular hearth within the four-columned hall expresses the ‘quaternity of the One’, one of the oldest religious symbols of humanity. Zeus is revealed in the ‘fiery monadic unit-cubit’ as an all-embracing god next to goddess Hestia, symbolised by the circular hearth. The ‘megaron’ expresses the alchemical quaternity and the triad but also the psychological stages of development in the process towards wholeness. In the Conclusions it is emphasised that the Mycenaean citadel was created as if in a repetition of a cosmogony. It is a ‘mandala’, the universal image which is identified with God-image in man. Moreover it is built in order to be experienced by its citizen in the process of his psychological transformation towards the ‘self’, the divine element within the psyche which unites with the divinely ordered Cosmos

Spike-timing dependent plasticity and connectivity in primate sensorimotor cortex

Thesis (Ph.D.)--University of Washington, 2016-06

Multipartite entanglement in harmonic oscillators subjected to dissipative quantum dynamics

Una detallada descripción de la dinámica de bajas energías del entrelazamiento multipartito es proporcionada para sistemas armónicos en una gran variedad de escenarios disipativos. Sin hacer ninguna aproximación central, esta descripción yace principalmente sobre un conjunto razonable de hipótesis acerca del entorno e interacción entorno-sistema, ambas consistente con un análisis lineal de la dinámica disipativa. En la primera parte se deriva un criterio de inseparabilidad capaz de detectar el entrelazamiento k-partito de una extensa clase de estados gausianos y no-gausianos en sistemas de variable continua. Este criterio se emplea para monitorizar la dinámica transitiva del entrelazamiento, mostrando que los estados no-gausianos pueden ser tan robustos frente a los efectos disipativos como los gausianos. Especial atención se dedicada a la dinámica estacionaria del entrelazamiento entre tres osciladores interaccionando con el mismo entorno o diferentes entornos a distintas temperaturas. Este estudio contribuye a dilucidar el papel de las correlaciones cuánticas en el comportamiento de la corrientes energéticas.

Research-based spin-offs as agents of knowledge dissemination: evidence from the analysis of innovation networks

The paper addresses the role played by research-based spin-offs (RBSOs) as knowledge dissemination mechanisms, through their position in knowledge networks. For this purpose the paper analyses the formal networks established by the Portuguese RBSOs in the context of publicly funded research, technology and pre-commercial product development projects, and investigates their configuration along two levels. At organisational level, in order to understand whether RBSOs extend their reach beyond the academic sphere; and if they do, whether they relate with similar firms or connect to organisations located downstream in the knowledge value chain, and which is their position in networks involving both research organisations and other firms. At spatial level, in order to understand whether RBSOs extend their reach beyond the region where they are created, thus potentially acting as connectors between diverse regions. The analysis starts from the population of RBSOs created in Portugal until 2007 (387) and identifies those that have established formal technological relationships as part of projects funded by all the programmes launched in the period 1993-2012. As a result, the analysis encompasses 192 collaborative projects and involves 82 spin-offs and 281 partners, of which only 20% are research organisations, the remaining being other firms and a variety of other user organisations. The results, although still preliminary, provide some insights into the knowledge networking behaviour of the RBSOs. As expected, research organisations are a central actor in spin-offs’ networks, being the sole partner for some of them. But half of the RBSOs have moved beyond the academic sphere, being frequently a central element in tripartite technological relationships between research and other organisations and occupying an intermediation position in the network, thus potentially acting as facilitators in knowledge circulation and transformation. Also as expected, RBSOs are predominantly located in the main metropolitan areas and tend to relate with organisations similarly located. But while geographical proximity emerges as important in the choice of partners, in about half of the cases, RBSOs knowledge networks have extended beyond regional boundaries. Given their central position in the network this suggests a role as connectors across regions that will be explored in subsequent research.

Research-based spin-offs as agents of knowledge dissemination: evidence from the analysis of innovation networks

The paper addresses the role played by research-based spin-offs (RBSOs) as knowledge dissemination mechanisms, through their position in knowledge networks. For this purpose the paper analyses the formal networks established by Portuguese RBSOs, in the context of publicly funded research, technology and pre-commercial product development projects, and investigates their configuration across two levels. At organisational level, in order to understand whether RBSOs extend their reach beyond the academic sphere; and if they do, whether they connect to organisations located downstream in the knowledge value chain, and which is their position in networks involving both research organisations and other firms. At spatial level, in order to understand whether RBSOs extend their reach beyond the region where they are created, thus potentially acting as connectors between diverse regions. The analysis starts from the population of RBSOs created in Portugal until 2007 (327 firms) and identifies those that have established formal technological relationships, as part of projects funded by all the relevant programmes launched in the period 1993-2012. As a result, the analysis encompasses 192 collaborative projects and involves 82 spin-offs and 281 partners, of which only 20% are research organisations, the remaining being other firms and a variety of other downstream organisations. The results, although still preliminary, provide some insights into the knowledge networking behaviour of the RBSOs. As expected, research organisations are a central actor in spin-offs’ networks, being the sole partner for some of them. But half of the RBSOs have moved beyond the academic sphere, being frequently a central element in tripartite technological relationships between research and other organisations, and occupying an intermediation position in the network, thus potentially acting as facilitators in knowledge circulation and transformation. Also as expected, RBSOs are predominantly located in the main metropolitan areas and tend to relate with organisations similarly located. But while geographical proximity emerges as important in the choice of partners, in about half of the cases, RBSOs knowledge networks have extended beyond regional boundaries. Given their central position in the network, this suggests a role as connectors across regions that will be explored in subsequent research.

First complete genome sequence of a capsicum chlorosis tospovirus isolate from Australia with an unusually large S RNA intergenic region

The first complete genome sequence of capsicum chlorosis virus (CaCV) from Australia was determined using a combination of Illumina HiSeq RNA and Sanger sequencing technologies. Australian CaCV had a tripartite genome structure like other CaCV isolates. The large (L) RNA was 8913 nucleotides (nt) in length and contained a single open reading frame (ORF) of 8634 nt encoding a predicted RNA-dependent RNA polymerase (RdRp) in the viral-complementary (vc) sense. The medium (M) and small (S) RNA segments were 4846 and 3944 nt in length, respectively, each containing two non-overlapping ORFs in ambisense orientation, separated by intergenic regions (IGR). The M segment contained ORFs encoding the predicted non-structural movement protein (NSm; 927 nt) and precursor of glycoproteins (GP; 3366 nt) in the viral sense (v) and vc strand, respectively, separated by a 449-nt IGR. The S segment coded for the predicted nucleocapsid (N) protein (828 nt) and non-structural suppressor of silencing protein (NSs; 1320 nt) in the vc and v strand, respectively. The S RNA contained an IGR of 1663 nt, being the largest IGR of all CaCV isolates sequenced so far. Comparison of the Australian CaCV genome with complete CaCV genome sequences from other geographic regions showed highest sequence identity with a Taiwanese isolate. Genome sequence comparisons and phylogeny of all available CaCV isolates provided evidence for at least two highly diverged groups of CaCV isolates that may warrant re-classification of AIT-Thailand and CP-China isolates as unique tospoviruses, separate from CaCV.

Molecular and biological characterisation of orthobunyaviruses

Orthobunyaviruses are the largest genus within the Bunyaviridae family, with over 170 named viruses classified into 18 serogroups (Elliott and Blakqori, 2001; Plyusnin et al., 2012). Orthobunyaviruses are transmitted by arthropods and have a tripartite negative sense RNA genome, which encodes 4 structural proteins and 2 non-structural proteins. The non-structural protein NSs is the primary virulence factor of orthobunyaviruses and potent antagonist of the type I interferon (IFN) response. However, sequencing studies have identified pathogenic viruses that lack the NSs protein (Mohamed et al., 2009; Gauci et al., 2010). The work presented in this thesis describes the molecular and biological characterisation of divergent orthobunyaviruses. Data on plaque morphology, growth kinetics, protein profiles, sensitivity to IFN and activation of the type I IFN system are presented for viruses in the Anopheles A, Anopheles B, Capim, Gamboa, Guama, Minatitlan, Nyando, Tete and Turlock serogroups. These are complemented with complete genome sequencing and phylogenetic analysis. Low activation of IFN by Tete serogroup viruses, which naturally lack an NSs protein, was also further investigated by the development of a reverse genetics system for Batama virus (BMAV). Recombinant viruses with mutations in the virus nucleocapsid protein amino terminus showed higher activation of type I IFN in vitro and data suggests that low levels of IFN are due to lower activation rather than active antagonism. The anti-orthobunyavirus activity of IFN-stimulated genes IFI44, IFITMs and human and ovine BST2 were also studied, revealing that activity varies not only within the orthobunyavirus genus and virus serogroups but also within virus species. Furthermore, there was evidence of active antagonism of the type I IFN response and ISGs by non-NSs viruses. In summary, the results show that pathogenicity in man and antagonism of the type I IFN response in vitro cannot be predicted by the presence, or absence, of an NSs ORF. They also highlight problems in orthobunyavirus classification with discordance between classical antigen based data and phylogenetic analysis.