[pt] A pesquisa intitulada Porque elas aparentam ser meninas ou agem como meninas: apagamento de identidades não-binárias em traduções do mangá Houseki no kuni analisa cinco traduções do referido mangá – duas traduções profissionais, uma para o inglês e uma para o francês; e três traduções amadoras, uma para o português, uma para o espanhol e uma para o inglês – e como essas lidaram com a não-binariedade dxs personagens. O objetivo foi examinar as maneiras nas quais ideologias hegemônicas de tradução e cis-heteronormativas podem levar ao apagamento de identidades LGBTQAI(mais). A análise dos dados demonstrou que todas as traduções para línguas neolatinas, assim como a tradução amadora para o inglês designaram um gênero axs personagens. No caso das línguas neolatinas, a análise dos meta e paratextos sugerem que o gênero gramatical dessas línguas desempenhou um papel importante no apagamento da não-binariedade de gênero. Contudo, também se verificou evidências da influência de ideologias cis-heteronormativas na escolha das estratégias tradutórias empregadas. Dentre as traduções analisadas, apenas a tradução profissional para o inglês não designou um gênero axs personagens. Contudo, a análise de fontes metatextuais revelou que ideologias de tradução relacionadas à ideia de fluência estavam por trás das estratégias tradutórias utilizadas, resultando em uma tradução que mantém a não-binariedade, porém, não a visibiliza. Ao estudar as ideologias cis-heteronormativas e de tradução que subjazem às estratégias tradutórias empregadas, a presente pesquisa contribui para entender como identidades LGBTQAI(mais) podem ser facilmente apagadas em traduções e propor formas de visibilizá-las a fim de combater a hegemonia cis-heteronormativa. / [en] The research entitled Because they look like girls or act like girls: erasure of non-binary identities in translations of the Houseki no kuni manga analyzes five translations of the referred manga - two professional translations, one into English and one into French ; and three amateur translations, one into Portuguese, one into Spanish and one into English - and how they dealt with the non-binary gender of the characters. The objective was to examine the ways in which cis-heteronormative ideologies and hegemonic translation ideologies can lead to the erasure of LGBTQAI (plus) identities. The analysis of the data showed that all the translations to Neo-Latin languages, as well as the amateur translation into English designated a gender to the characters. In the case of Neo-Latin languages, the analysis of meta and paratexts suggests that the grammatical gender of these languages played an important role in erasing the non-binary gender of the characters. However, there was also evidence of the influence of cis-heteronormative ideologies in the choice of translation strategies employed. Among the translations analyzed, only the professional translation into English did not designate a gender to the characters. However, the analysis of metatextual sources revealed that translation ideologies related to the idea of fluency were behind the translation strategies used, resulting in a translation that maintains the non-binary gender of the characters, but does not make it visible. By studying the cis-heteronormative and translation ideologies that underlie the translation strategies employed, this research contributes to understand how LGBTQAI (plus) identities can be easily erased in translations and propose ways to make them visible in order to fight cis-heteronormative hegemony.

CD2 is a transmembrane molecule and a “non-canonical” member of the signaling lymphocyte activation molecule (SLAM) family of receptors that is expressed on T cells and NK cells. Its ligands, mouse CD48 and human CD58, are widely expressed on hematopoietic cells including antigen-presenting cells (APCs) and T cells. Previous studies indicated that CD2 promotes T-cell receptor (TCR) signaling when it is engaged by its ligands displayed on APCs. However, the supporting experimental data were rather controversial, and there is no general agreement about the role of CD2 in T cell activation. To study the function of CD2 and its ligands in T cells, we examined T cell functions in newly generated mouse strains lacking CD2 or CD48 in the C57BL/6 background. Compared to wild-type (WT) mice, T cells from CD2-deficient (“knock-out”; KO) mice had severe activation defects. Surprisingly, expression of CD48 on T cells, not on APCs, was also necessary for optimal T cell responses. We found evidence of CD2 interacted with CD48 in cis on T cells and observed their co-localization by confocal microscopy and fluorescence resonance energy transfer (FRET). The only exception was CD2-dependent cytotoxicity, which required CD48 both on T cells and on APCs. Mechanistic studies using mass spectrometry and structure-function analyses revealed that the cis interactions between CD2 and CD48 on T cells boosted TCR signaling, an effect that correlated with the capacity of CD2 to recruit the kinase Lck. Similarly, our further study revealed that the cis interactions between CD2 and CD58 on human T cells were also necessary for maximal TCR signaling and T cell activation. Taken together, our studies provide clear evidence that cis interactions between CD2 and its ligands on T cells are important in TCR signaling and T cell activation. Modulation of these cis interactions can be a promising approach to suppress or enhance T cell activation in a therapeutic setting. / CD2 est une molécule transmembranaire et un membre “ non-canonique ” de la famille de la famille SLAM (« signaling lymphocyte activation molecule ») exprimée à la surface des lymphocytes T et des cellules NK (« natural killer »). Les ligands de CD2, CD48 chez la souris et CD58 chez l’humain, sont exprimés de manière ubiquitaire sur les cellules hématopoïétiques, y compris sur les cellules présentatrices d’antigène (CPA) et lymphocytes T. Des études antérieures ont indiqué que CD2 est impliqué dans la signalisation des récepteurs TCR (« T-cell receptor ») en réponse à son engagement par CD48 sur le CPA; cependant, les données expérimentales qui supportent ce modèle sont plutôt contradictoires et aucun accord n’a été trouvé sur les rôle de CD2 dans l’activation de lymphocytes T. Pour étudier la fonction de CD2 et ses ligands, nous avons examiné les fonctions des lymphocytes T chez des souches de souris dépourvues de CD2 ou CD48 nouvellement générées à partir du “fond génétique” C57BL/6. Par rapport aux souris de type sauvage (WT; « wild-type »), les lymphocytes T de souris CD2-déficientes (« knock-out »; KO) présentent des sévères défauts d’activation. Il est intéressant de noter que l’expression de CD48 sur les lymphocytes T, mais non sur les CPA, était aussi nécessaire pour les réponses des lymphocytes T. Nous avons également démontré que CD2 interagit en cis avec CD48 sur les cellules T et avons observé leur co-localisation par microscopie confocale et FRET (« fluorescence resonance energy transfer) ». La seule exception était la cytotoxicité CD2- dépendante, qui nécessitait l’expression de CD48 à la fois sur les lymphocytes T et sur les CPA. L’étude des mécanismes par la spectrométrie de masse et les analyses structurefonction ont démontré que les interactions en cis entre CD2 et CD48 permettent de stimuler la signalisation du TCR, ce qui corrèle avec la capacité de CD2 à recruter la kinase Lck. De manière similaire, notre étude plus approfondie a démontré que les interactions en cis entre CD2 et CD58 sur les lymphocytes T humains sont nécessaires pour la signalisation maximale du TCR et l’activation cellulaire T. L’ensemble de nos études ont mis en évidence que les interactions en cis entre CD2 et ses ligands sur les lymphocytes T jouent un rôle important dans la signalisation du TCR et l’activation de ces cellules. La modulation de ces interaction en cis pourrait être une approche potentielle pour augmenter ou interférer avec l’activation des lymphocytes T dans un contexte thérapeutique.

No description available.

Die vorliegende Arbeit untersucht mit bioinformatischen Methoden die biologische Bedeutung von Ähnlichkeiten in Kleinstrukturen und peptidischen Sequenzmotiven sowie lokaler und globaler Sequenzähnlichkeit. Der erste Teil der Arbeit behandelt chemische Ähnlichkeiten. Ausgehend von bekannten Inhibitoren der Fehlfaltung des Prionproteins wurde eine Datenbank pharmakologischer Wirkstoffe nach chemisch und strukturell ähnlichen Substanzen durchsucht und 16 Substanzen als neue potentielle Inhibitoren der Fehlfaltung vorgeschlagen. Der nächste Teil untersucht Ähnlichkeiten in Sequenzmotiven, die eine Interaktion mit Pex19, dem Importrezeptor für peroxisomale Membranproteine, vermitteln. In Zusammenarbeit mit einer experimentellen Arbeitsgruppe konnte die Bindestelle charakterisiert und Präferenzen für bestimmte Aminosäuren herausgearbeitet werden. Das Bindemotiv ist eine vermutlich helikale Region mit verzweigtkettigen aliphatischen und basischen Aminosäuren. Aus experimentellen Daten konnte eine positionsabhängige Vorhersagematrix erstellt und validiert werden. Die Beziehung zwischen lokalen Sequenzähnlichkeiten und der Konformation von Prolylbindungen in Proteinen ist Thema des dritten Teils. Die Aminosäurepräferenzen in der Nachbarschaft von cis- und trans-Prolylresten unterscheiden sich, und beide zeigen unterschiedliche Austauschpräferenzen bei Mutationen. Im Gegensatz zu lokaler Sequenzähnlichkeit ist eine globale Sequenzähnlichkeit von nur 20% ein wesentlich besserer Indikator für das Auftreten von cis-Prolylbindungen. Der letzte Teil befaßt sich mit inverser Sequenzähnlichkeit zwischen Proteinen, die wesentlich öfter auftritt als erwartet. Proteine aus einem nichtredundanten Datensatz wurden gleich- und gegenläufig aligniert und strukturelle Ähnlichkeiten zwischen den aufgefundenen Proteinpaaren untersucht. Es konnte gezeigt werden, daß bis auf kurze Sekundärstruktur-Einheiten eine inverse Sequenzähnlichkeit zwischen Proteinen keine strukturelle Ähnlichkeit impliziert. / This work is dealing with the biological impact of similarities between chemical structures, protein sequence motifs and local sequence surrounding as well as global sequence similarity. All four aspects are analyzed by computational methods. The first part is dealing with chemical similarities. Based on a recently published set of prion protein misfolding inhibitors, a data base of approved drugs has been screened for compounds with chemical and structural similarities to these substances. 16 drugs are proposed as new potential inhibitors of prion protein aggregation. The next part addresses similarities of sequence motifs which mediate the interaction with the peroxisomal membrane protein import receptor Pex19. In cooperation with an experimental group, the binding site could be characterized, and amino acid preferences of the different positions of the motif have been determined. The binding motif is a probably helical region of target proteins bearing branched aliphatic and basic residues. A position specific scoring matrix for the prediction of Pex19 binding sites could be generated and validated. The relation between local sequence similarity and prolyl bond conformation is examined in the third part. Amino acid preferences of neighboring residues differ between cis and trans prolyl residues, and both species show different amino acid exchange patterns upon mutation. In contrast to local sequence similarity, overall sequence similarity between proteins as low as 20% is a much better indicator for the occurrence of cis prolyl bonds. The last part focuses on inverse sequence similarity between proteins which occurs far more often than expected by chance. Proteins from a nonredundant data set have been aligned in parallel and antiparallel, and structural similarities between the detected protein pairs have been examined. It could be shown that, with the exception of short secondary structural elements, inverse sequence similarity does not imply structural similarity.

Cis-regulatorische Elemente wie Promotoren und Enhancer, die die Regulation der Transkription von Genen steuern, befinden sich in Regionen des dekondensierten Chromatins. DNase-seq und ATAC-seq sind weit verbreitete Verfahren, um solche offenen Chromatinregionen genomweit zu untersuchen. Die einzel-Nukleotid-Auflösung von DNase-seq wurde des Weiteren genutzt, um Transkriptionsfaktor-Bindungsstellen (TFBS) in regulatorischen Regionen durch TF-Footprinting zu bestimmen. Kürzlich durchgeführte Studien haben jedoch gezeigt, dass DNase I einen Sequenzbias aufweist, welcher nachteilige Auswirkungen auf die Footprinting-Effizienz hat. Auch wurden das Footprinting und die Auswirkungen des Sequenzbias auf ATAC-seq noch nicht umfassend untersucht. In dieser Arbeit nehme ich einen systematischen Vergleich der beiden Methoden vor und zeige, dass die beiden Methoden unterschiedliche Sequenzbiases haben und korrigiere diese protokollspezifischen Biases beim Footprinting. Der Einfluss von Bias-Korrekturen der Footprinting Ergebnisse ist für DNase-seq größer als für ATAC-seq, und Footprinting mit DNase-seq führt zu besseren Ergebnissen in unserer Datensätze. Trotz dieser Unterschiede zeige ich, dass die Integration replizierter Experimente die Ableitung von qualitativ hochwertigen Footprints ermöglicht, wobei die beiden Techniken weitgehend übereinstimmen. Diese Techniken werden ferner eingesetzt, um die cis-regulatorischen Elemente zu charakterisieren, die die Embryogenese der Fruchtfliege Drosophila melanogaster bestimmen. Durch die Verwendung von Embryonen die sich im richtigen Entwicklungsstadium befinden, sowie gewebespezifischer Kernsortierung mit offenem Chromatin-Profiling können zeitlich und gewebespezifisch aufgelöste vermeintliche cis-regulatorische Elemente definiert werden. Zusammengenommen demonstrieren diese Analysen die Fähigkeit der offenen Chromatin-Profilierung und der Computeranalyse zur Aufklärung der Mechanismen der Genregulation. / Cis-regulatory elements such as promoters and enhancers, that govern transcriptional gene regulation, reside in regions of open chromatin. DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBS) in regulatory regions through TF footprinting. However, recent studies have demonstrated the sequence bias of DNase I and its adverse effects on footprinting efficiency. Furthermore, footprinting and the impact of sequence bias have not been extensively studied for ATAC-seq. In this thesis, I undertake a systematic comparison of the two methods and demonstrate that the two methods have distinct sequence biases and correct for these protocol-specific biases when performing footprinting. The impact of bias correction on footprinting performance is greater for DNase-seq than for ATAC-seq, and footprinting with DNase-seq leads to better performance in our datasets. Despite these differences, I show that integrating replicate experiments allows the inference of high-quality footprints, with substantial agreement between the two techniques. These techniques are further employed to characterize the cis-regulatory elements governing the embryogenesis of a complex organism, the fruit fly Drosophila melanogaster. Combining tight staging of embryos and tissue-specific nuclear sorting with open chromatin profiling, enables the definition of temporally and tissue-specifically resolved putative cis-regulatory elements. Taken together, these analyses demonstrate the power of open chromatin profiling and computational analysis in elucidating the mechanisms of transcriptional gene regulation.

Thesis (MA (Psychology))--University of Stellenbosch, 2005. / The current study investigates intercultural differences in suggestibility between Black, Coloured and White students at a South African university using the Creative Imagination Scale (CIS), (Wilson & Barber, 1978). The CIS and a short biographical questionnaire measuring embeddedness in traditional culture were administered to three samples (N=20 each) from students belonging to the above cultural groups. Statistical tests were applied to determine the effects of ethnicity, cultural embeddedness and gender on CIS scores. The results indicate that these three dimensions do not significantly impact on CIS scores. Implications of the results obtained are discussed and ensuing recommendations for future related research are made.

Cyclophilins are ubiquitous enzymes that are involved in protein folding, signal transduction, viral proliferation, oncogenesis, and regulation of the immune system. Cyclophilin A is the prototype of the cyclophilin family. We use molecular dynamics to describe the catalytic mechanism of cyclophilin A in full atomistic detail by sampling critical points along the reaction coordinate, and use accelerated molecular dynamics to sample cis-trans interconversions. At these critical points, we analyze the conformational space sampled by the active site, flexibility of the enzyme backbone, and modulation of binding interactions.We use Kramer’s rate theory to determine how diffusion and free energy contribute to lowering the activation energy of prolyl isomerization. We also find preferential binding modes of several cyclophiln A inhibitors, and compare the conformational space sampled by inhibited cyclophilin A to the conformational space sampled during wild-type interactions. We also analyze the mechanism of the next family member cyclophilin B in order to probe differences in enzyme dynamics and intermolecular interactions that could possibly be exploited in isoform-specific drug design. Our results indicate that cyclophilin proceeds by a conformational selection binding mechanism that manipulates substrate sterics, electrostatic interactions, and multiple reaction timescales in order to speed up reaction rate. Conformational space sampled by cyclophilin when inhibited and when undergoing wild-type interactions share significant similarity. Cyclophilins A and B do have notable differences in enzyme dynamics, due to variation in intramolecular interactions that arise from variation in primary structures. This work demonstrates how computational methods can be used to clarify catalytic mechanisms.

The tautomerase superfamily is composed of a group of proteins characterized by two key features: the N-terminal proline and a beta-alpha-beta-motif. This superfamily has been divided into five families represented by 4-oxalocrotonate tautomerase (4-OT), 5-(carboxymethyl)-2-hydroxymuconate isomerase (CHMI), cis-3-chloroacrylic acid dehalogenase (cis-CaaD), malonate semialdehyde decarboxylase (MSAD), and macrophage migration inhibitory factor (MIF). Cg10062 is a homologue of cis-CaaD, but has several distinct biochemical properties from cis-CaaD. For example, Cg10062 can be irreversibly inhibited by (R)- or (S)-oxirane-2-carboxylate, whereas cis-CaaD can only be irreversibly inhibited by (R)-oxirane-2-carboxylate. FG41MSAD is a homologue of MSAD, with comparable decarboxylase activity but missing Arg-73 known to be crucial for the MSAD activity. In order to understand the unique biochemical characteristics of Cg10062 and FG41MSAD, we have solved five crystal structures. These crystal structures have established a solid structural basis for understanding the mechanisms of their activities. The eukaryotic protein phosphatases are composed of a group of proteins that are responsible for reversible phosphorylation. The eukaryotic protein phosphatases have been divided into three families, the phosphoprotein phosphatase (PPP) family, the protein phosphatase Mg2+- or Mn2+-dependent (PPM) family and the protein Tyr phosphatase (PTP) family. PDP1 is a member of PPM family. PDP1 is also an important component of the large pyruvate dehydrogenase complex (PDC) which catalyzes the decarboxylation of pyruvate to yield acetyl-CoA with the accompanying reduction of NAD+. In order to understand the mechanism in which it dephosphorylates its target protein we have solved the structure of the catalytic domain of PDP1. Analysis of these structures in the light of their evolutionary contexts enables us to appreciate the unity and diversity of the biological systems at the chemical level and help us solve interesting problems, such as the possible physiological functions for some members within the tautomerase superfamily. / text

The expansion of gene-specific trinucleotide repeats is responsible for a growing list of human disorders, including myotonic dystrophy type 1 (DM1). Repeat instability for most of these disorders, including DM1, is characterized by complex patterns of inherited and ongoing tissue-specific instability and pathogenesis. While the mechanistic basis behind the unique locus-specific instability of trinucleotide repeats is currently unknown, DNA metabolic processes are likely to play a role. My thesis involves investigating the contribution of DNA replication to the trinucleotide instability of myotonic dystrophy type 1. Herein I have designed an in vivo primate model system, based on the SV40 replication system, to assess the contribution of DNA replication to DM1 repeat instability. This system allows the assessment, under controlled conditions, and manipulation of variables that may affect replication-associated repeat instability, under a primate cellular system. Using the SV40 model system, I not only confirmed previous observations that repeat length and replication direction affect repeat instability, but also for the first time determined that the location of the replication origin relative to the repeat tract plays an important role in repeat instability. This novel observation allowed for the development of a fork-shift model of repeat instability, in which cis-elements adjacent to the repeat tract affect replication, in turn altering the propensity for repeat instability. To further my study of DNA replication in DM1 repeat instability, I have mapped the origin of replication adjacent to the DM1 locus in human patient cells and the tissues of DM1 transgenic mice actively undergoing repeat instability. The position of the replication origins adjacent to the repeat tract at the DM1 locus places several known cis-elements, including CTCF binding sites, in a position to alter replication as predicted by the fork-shift model. My analysis of the CTCF sites showed them capable of altering replication and repeat instability at the DM1 locus. Taken together these results suggest that the placement of replication origins, repeat tracts and cis-elements, may mark trinucleotide repeat tracts, such as the DM1, for locus-, tissue- and development-specific replication-associated repeat instability.

Winter rye produces ice-modifying antifreeze proteins upon cold treatment. Two of these antifreeze proteins are members of the large, highly conserved, ??-1,3-endoglucanase family. This project was designed to identify glucanase genes that are expressed during cold acclimation, wounding, pathogen infection, drought or treatment with the phytohormones ethylene and MeJa. Additionally, a more detailed proteomic analysis was to be carried out to evaluate the glucanase content of the apoplast of cold-acclimated (CA) winter rye. Results of 2D SDS-PAGE analysis revealed that non-acclimated whole leaf protein extracts contain at least two ??-1,3-endoglucanses while CA whole leaf protein extracts contain at least three ??-1,3-endoglucanses. Subsequent 2D SDS-PAGE analysis was conducted on the apoplast extracts of NA and CA winter rye plants revealed the limitations of standard 1D SDS-PAGE. The 2-dimensional gel analysis revealed that there is a minimum of 25 proteins within the apoplast of CA winter rye, including at least 5 ??-1,3-endoglucanases. Genome walking was used to isolate cold-responsive glucanase genes. The five genes isolated were designated scGlu6, scGlu9, scGlu10, scGlu11 and scGlu12. The cis-element pattern within the promoter of each gene was evaluated using online databases of documented plant cis elements. As expected, all of the promoters contained elements associated with cold, biotic and abiotic stresses, light regulation, and development. The expression patterns predicted by the cis elements in each promoter were compared to the mRNA abundance produced by each gene as detected by semi-quantitative reverse transcriptase PCR. In most cases, the abundance of transcripts arising from each gene loosely corresponded to the expression pattern predicted by the cis elements the corresponding promoter. Transcripts of scGlu9, 10 and 11 were present in cold-treated tissues and are candidates for ??-1,3-endoglucanases with antifreeze activity. The results presented in this thesis provide additional insight into the apoplast proteome of CA winter rye plants as well as the complexity of the signals controlling the proteins that reside there. Although there are still a number of unresolved questions, this research opens new directions for future studies in the cold acclimation process in winter rye and specifically for the contribution of ?? -1,3-endoglucanses.