Thesis advisor: Michelle M. Meyer / Non-coding RNA (ncRNA) perform vital functions in cells, but the impact of diversity across structure and function of homologous motifs has yet to be fully investigated. One reason for this is that the standard phylogenetic analysis used to address these questions in proteins cannot easily be applied to ncRNA due to their inherent characteristics. Compared to proteins, ncRNA have shorter sequence lengths, lower sequence conservation, and secondary structures that need to be incorporated into the analysis. This has necessitated an effort to develop methodology for investigating the evolutionary and functional relationship between sets of ncRNA. In this pursuit, I studied closely related riboswitches. Riboswitches are structured ncRNA found in bacterial mRNA that regulate gene expressions using their two major components: the aptamer and the expression platform. The aptamer of a riboswitch is able to bind a specific small molecule (ligand), and the bound/unbound state of the aptamer influences conformational changes in the expressions platform that can lead to increased or decreased downstream gene expression. Utilizing sequence and structural similarity metrics combined with graph clustering and de novo community detection algorithms I have determined a methodology for investigating the functional and evolutionary relationship between closely related riboswitches, and other ncRNA by extension, that are found across a range of diverse phyla. / Thesis (PhD) — Boston College, 2021. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (p. 83-102).

Human immunodeficiency virus type 1 (HIV-1) is a member of the lentivirus subfamily of retroviruses. HIV-1 expresses multiple genes from a single provirus by alternative splicing. Early in viral expression, fully spliced 2-kb viral RNA is exported from the nucleus and encodes the viral regulatory protein, Rev, which is essential for nuclear transport of partially spliced and unspliced genomic-length RNA. Rev binds to an RNA structural element called the Rev response element (RRE) and mediates nuclear export through the leucine-rich nuclear export signal (NES) pathway. The human Rev Interacting Protein (hRIP) interacts specifically with the Rev NES. Rev NES mutants that are unable to export Rev-dependent RNAs are also unable to bind to hRIP. The hRIP cDNA encodes a 562 amino acid protein containing an N-terminal zinc finger with homology to Arf GAP domains, a central serine and threonine rich region, and C-terminal phenylalanine-glycine (FG) repeats characteristic of nucleoporins. To identify an hRIP ortholog in a genetically tractable organism, we performed database searches using the N-terminal zinc finger of hRIP. Using this approach, we identified a novel gene in Schizosaccharomyces pombe. Alignment of the entire reading frame of the putative ortholog with hRIP indicates similarity with the serine/threonine rich region and with the FG repeats, suggesting that S. pombecould be a good model system to study the cellular function of hRIP. We find that the S. pombe ORF is an essential gene, which encodes a 483 amino acid protein that is also able to interact with the NES of HIV-1 Rev. Based on being an essential gene, and the presence of a putative Arf GAP domain, the ORF was named an Arf GAP essential for viability, agv1+. We show that Agv1 is not directly involved in the nuclear export of poly(A+) RNA or 5S rRNA, nuclear export of leucine-rich NES-containing proteins, or nuclear import of nuclear localization signal (NLS)-containing proteins. However, Agv1 does appear to play a role in the cytoplasmic localization of 5S rRNA. We demonstrate that loss of Agv1 alters the localization of endoplasmic reticulum (ER) membrane and Golgi membrane resident proteins, accumulates intracellular membrane, and blocks processing of carboxypeptidase Y. Furthermore, the S. cerevisiae ADP-ribosylation factor (Arf) GTPase activating protein (GAP) Glo3, but not a catalytically inactive Glo3 mutant [R59K], is able to partially compensate for the loss of Agv1 function in temperature sensitive strains, indicating that Agv1 is an S. pombe Arf GAP with some functional features similar to S. cerevisiae Glo3.

Depuis les premières formes d’urbanisme, les villes sont façonnées par des constructions idéologiques qui impactent sur le quotidien des individus et sur les ségrégations socio-spatiales. Notre questionnement général porte sur ce contexte, et plus particulièrement sur la façon dont s’objectivent les différentes positions occupées dans la structure sociale par les représentations et les pratiques quotidiennes de l’espace urbain. L’étude de cinq différentes représentations socio-spatiales au sein des agents de l’Université de Strasbourg aura permis de mettre en évidence l’existence d’un principe d’homologie structurale entre les dimensions cognitives, spatiales et sociales de la relation individu-milieu. Certains groupes entretiennent une relation fonctionnelle à la ville traduisant la complexité des lieux fréquentés. À l’inverse, d’autres groupes entretiennent une relation évaluative qui se détache des fréquentations pour se concentrer sur des lieux plus ou moins « emblématiques ». Or, ces deux rapports distinguent les identités sociales de ces groupes. Lorsque les premiers sont dominés et peuvent se valoriser par leurs pratiques, les seconds sont dominants et le peuvent par une comparaison à d’autres villes qui se rapproche de l’idéologie de la ville-mondiale. Les enjeux identitaires des représentations et pratiques spatiales socialement intériorisées participeraient ainsi aux ségrégations. / Ever since the earliest forms of urbanism, cities have been shaped by ideological constructs that impact the everyday life of individuals and socio-spatial segregations. This PhD thesis focuses specifically on how positions in the social structure are objectified in the representations and everyday practice of urban space. Based on study of five different socio-spatial representations among University of Strasbourg staffers, it evidences a principle of structural homology between the cognitive, spatial and social dimensions of the individual-environment relationship. Some groups have a functional relationship to the city that reflects the complexity of the places they frequent. Conversely, others have an evaluative relationship that focuses on ‘emblematic’ places. These two relationships are markers of these groups’ social identities. Whereas the former are dominated and may seek to enhance their status through their practices, the latter are dominant and do so by making reference to the global city and comparing their city to others. The identity stakes of socially internalized spatial practices and representations ultimately contribute to segregation.