published_or_final_version / abstract / Microbiology / Master / Master of Philosophy

Hepatitis C virus NS5A is a multi-functional viral protein essential for viral replication and assembly, although the exact role the protein plays in the viral lifecycle remains unclear. A vast array of functions have been attributed to NS5A in recent years, despite the lack of enzymatic activity. NS5A has been found to interact with over 130 host proteins including many which are central to cellular signaling pathways. NS5A is composed of three domains separated by regions of low complexity. All three domains perform important functions in the viral lifecycle. Domains I and II are essential for viral replication whereas domain III is required for viral assembly. However, the role that NS5A and its individual domains may play in modulating viral translation remains controversial. Previous studies have utilized translation reporter systems that do not accurately reflect the role of the viral 3´-UTR in modulating viral translation. We and others have shown that NS5A binds to the poly-U/UC region of the 3´-UTR. In addition to serving as the initiation site for negative strand synthesis the 3´-UTR functions to significantly enhance viral translation. The mechanism of translation enhancement remains unclear but may involve long range RNA-RNA interaction with the IRES, the binding of cellular proteins which stimulate translation and/or the recycling of ribosomes. Therefore, the protein-RNA interaction between NS5A and the poly-U/UC region has the potential to modulate viral translation. Therefore we set out to determine the role of NS5A and its individual domains in modulating viral translation and the role of the NS5A-poly-U/UC region interaction in this modulation. Utilizing monocistronic RNA reporters which contain the viral 5´- and 3´-UTRs and an internal Renilla luciferase reporter gene, we determined that NS5A specifically down-regulates viral translation in a dose-dependent manner through a mechanism dependent upon the presence of the poly-U/UC region in the viral 3´-UTR. Furthermore, we have re-tested the effect using full-length HCV genomic RNA reporters. These results suggest that NS5A is able to interfere with the stimulation of viral translation exerted by the 3´-UTR. This down-regulatory function of NS5A may function in mediating a switch from translation to replication, a step required in the lifecycle of a positive sensed RNA virus. Having established a role for NS5A in modulating viral translation, we then aimed to determine which region of NS5A was responsible for this effect. We found that each of NS5A domains was capable of this modulatory effect on viral translation independently. Although surprising, this finding is not entirely unexpected as each domain has been shown to retain the ability to bind to the poly-U/UC region. Within NS5A domain I we identified a 61 aa. region sufficient for translation down-regulation. Furthermore, we have identified a number of positively charged residues within this region involved in the modulation of viral translation, in particular arginine 112 (R112). This residue has previously been found to be at the domain I dimer contact interface and to form an intermolecular hydrogen bond with glutamic acid 148 (E148). We found that mutations R112A and E148A individually negate the ability of domain I to modulate viral translation and these mutations impede the formation of domain I dimers. Additionally, the R112A mutation appears to affect the ability of domain I to interact with the poly-U/UC region of the viral 3´-UTR alluding to the possible mechanism of translation modulation. Finally this mutation was lethal in an HCV subgenomic replication, confirming the link between NS5A dimerization, RNA binding and viral replication. These results collectively point to a crucial role for the NS5A arginine 112 residue in the modulation of HCV lifecycle by NS5A. Within NS5A domain II, we identified a 47 aa. region sufficient for translation modulation. Through the mutation of positively charged amino acids within this region, we found that lysine 312 (K312) was essential for this effect. The ability of this domain to modulate viral translation was completely lost when K312 was mutated within a full domain II protein fragment. The mechanism behind this modulation remains unclear but the 47 aa. region identified has been previously found to contain a region proposed to make contact with poly-U RNA and the K312 residue was suspected to interact directly with such RNA. Furthermore, this region interacts with the host protein cyclophilin A, an interaction that enhances the RNA binding ability of domain II. These findings strongly suggest that domain II modulates viral translation by binding within the poly-U/UC region. While investigating the modulation of viral translation by NS5A domain III we determined that the C-terminal 31 aa. are sufficient for the effect of this domain on viral translation. Through alanine scanning mutagenesis we identified glutamic acid 446 (E446) as playing a key role in the modulatory function of this region. Within a domain III protein fragment mutation of this E446 residue abolishes the modulatory function of this domain towards HCV translation. The mechanism behind this modulation and the role of E446 in this effect remains to be determined. These findings suggest that in addition to being essential for viral replication and assembly, NS5A has an important role in modulating viral translation through a mechanism requiring the poly-U/UC region of the viral 3´-UTR. Furthermore, each domain of NS5A appears to contribute to this effect. These results support the description of NS5A as a multi-functional protein and the further characterization of its functions may aid in the development of novel antivirals targeting the numerous functions of this complex, and at times puzzling, viral protein.

La protéine CIRP (Cold Induced RNA binding Protein) est une petite protéine de liaison à l’ARN de 172 acides aminés, qui est constituée du côté amino-terminal d’un domaine de liaison à l’ARN de type RRM (RNA recognition motif), et d’une partie carboxy-terminale riche en glycine et arginine qui comprend plusieurs motifs RGG. Elle a été identifiée comme étant inductible par hypothermie mais aussi par irradiation aux UV et par hypoxie. Nous avons analysé son expression et sa localisation en réponse à différents stress cellulaires. Nous avons montré qu’un traitement à l’arsénite qui induit un stress oxydant n’altère pas l’expression de CIRP provoque sa localisation dans les granules de stress (SG). Les SG sont des structures ribonucléoprotéiques cytoplasmiques contenant des complexes de pré-initiation incompétents pour la traduction, et qui s’accumulent dans les cellules exposées à un stress. Ces structures constituent des sites de triages des ARNm, dans lesquels les ARNm sont soit stockés en attente d’une réinitiation de la traduction une fois le stress surmonté, soit destinés à être dégradés. La protéine CIRP se localise dans les SG que ce soit suite à un stress cytoplasmique ou du réticulum endoplasmique. Nous avons montré également que la localisation de la protéine CIRP dans les SG se déroule indépendamment de la présence de la protéine TIA-1 qui a été décrite comme responsable de l’assemblage des SG. De plus la surexpression de la protéine CIRP conduit à la formation de SG. Nous suggérons donc qu’il existe plusieurs voies qui mènent à l’assemblage de ces structures. En outre, nous avons analysé la localisation de mutants par délétion de la protéine CIRP et avons montré que le domaine RRM et le domaine RGG peuvent indépendamment localiser la protéine dans les SG. Par contre, la méthylation des résidus arginine du domaine RGG est une modification nécessaire à la localisation de CIRP dans les SG. Ensuite, nous avons étudié la fonction de la protéine CIRP dans le métabolisme des ARN messagers. Nous avons montré par une méthode d’adressage, que CIRP est un répresseur de la traduction des ARNm et que le domaine carboxy-terminal est nécessaire et suffisant à cette fonction.

<p>This study investigates how best to solve difficulties that may arise when translating bird literature from English into Swedish. The focus of the study lies on the translation of attributive adjectives and bird terminology. The text chosen for the translation, which serves as the basis for the analysis, is the section on general habits of the <em>Turdidae-family </em>in the comprehensive work <em>Handbook of the Birds of the World. </em>Translation theory that proved helpful in the translation process and in the subsequent analysis was primarily that of Vinay and Darbelnet (1995, 2004), Nida (1964a) and Newmark (1981). In most cases a literal translation could be perfonned, both in regard to attributive adjectives and bird tenninology, however, in some cases other translation procedures, such as transposition and equivalence, proved useful. Attributive adjectives that could not be translated literally, or that were preferred not to be translated literally, were translated through the use of transposition, into for instance: compound nouns, prepositional phrases, relative clauses and <em>that-clauses. </em>Bird terminology for which no suitable corresponding terminology could be found in the target language, was translated non-literally through the use of equivalence, into structures maintaining the equivalent semantic meaning in a natural way.</p>

In eukaryotes, regulation of translation and decay of messenger RNA are critical for fine-tuned control of gene expression. An important point of control is the key transition where mRNAs exit translation and assemble into a non-translating mRNP state that can accumulate in cytoplasmic granules such as P bodies and/or Stress granules. In the budding yeast Saccharomyces cerevisiae , the activators of decapping Dhh1 and Pat1 appear to promote the exit of mRNAs from translation. In my work, summarized below, I describe a new regulator of translation repression and mRNA degradation, Stm1, and its novel mode of action. First, I identified Stm1 as a novel regulator of translation repression and mRNA decay. Stm1 shows several genetic interactions with Pat1 and Dhh1, in a manner consistent with Stm1 promoting the function of Dhh1. This suggests that Stm1 has a role to play in translation repression and/or activation of mRNA decay. stm1 δ strains are defective in the degradation of a subset of mRNAs that include EDC1 and COX17 . These results strongly argue that Stm1 is a novel addition to the mRNA degradation machinery. Second, I have shown that Stm1, a known ribosome-associated protein, can bind and stall 80S ribosomes to repress translation and promote decay. Stm1 is able to repress translation and stall an 80S complex in vitro . Several mutations were identified in the protein, which link the in vitrophenotype to its biological functionin vivo. The analysis of different steps in translation reveals Stm1 functions in a novel manner to inhibit translation after the formation of an 80S complex. Since most of the regulation of translation is thought to happen at the stage of initiation, this study reveals a novel mode of translation regulation. These results also provide a direct and mechanistic link between ribosome function, inhibition of translation and the degradation of messenger RNAs.

This is a dissertation project on medieval Arabic rhetoric and philosophy that focuses on the innovative nature of the knowledge produced while translating and commenting on foreign works of science and philosophy in Abbasid Baghdad. Chapter One challenges colonial attitudes toward the Translation Movement as exclusively imitative and preservative. The chapter shows that the translations had practical and ideological purposes to fulfill, not simply archival ones. Translation genres are discussed to show how deletions, additions, and new material were introduced during the translation process to ensure that that translation work met the goals of the sponsors. The work of the most renowned translator, Hunayn Ibn Ishaq is discussed in some detail to illustrate the process of translation and to show that translation overlapped with knowledge making. The chapter also covers the translation done in fields such as medicine, astronomy, and philosophy. Chapter Two covers how the work of theorists such as Edward Said, Michel Foucault, and Mikhail Bakhtin enabled me to challenge an Orientalist attitude toward medieval Arabic philosophy as was as show its innovative nature. In Chapter Three, I provide a translation of al-Kindi's "A Statement on the Soul," followed by an analysis of the epistemological and persuasive significance of the treatise. The chapter illustrates how the Arabic engagement with Greek and Neo-Platonic knowledge was dialogic in nature. Chapter Four is a translation of al-Farabi's book of rhetoric. Chapter Five is an analysis of al-Farabi's theory of rhetoric that is based on the previous chapter. It focuses on his understanding of rhetoric as a logical art, how logical and rhetorical terms acquired new meanings when translated from Greek to Arabic in his work, and the rhetorical nature of his work as he adapted Platonic and Aristotelian models to suit his monotheistic context.

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The aim of this research paper is to analyze the peculiarities of grammatical translation transformations in modern English novel “Bridget Jones’s Diary” (1996) written by Helen Fielding and its translated Lithuanian version. To achieve this aim the following objectives have been set: 1. To present the theoretical background about translation as a science. 2. To represent the linguistic theory about the role of grammar in translation practice. 3. To explain the usage of grammatical translation transformations in the target text. 4. To reveal the distribution of pure and mixed grammatical translation transformations in the intended text. The structure of the work. The theoretical part focuses on the issues of translation. initiating. Namely, the development of translation studies, equivalence, methods, procedures and translation transformations have been presented. In the subsequent part, i.e. the practical analysis, the usage of grammatical translation transformations has been briefly analyzed considering the collected instances. / Darbo tikslas išanalizuoti gramatinių vertimo transformacijų įpatybes šiuolaikinėje anglų kalbos noveleje "Bridžitos Džouns dienoraštis" (1996)parašytos Helen Fielding ir šios knygos lietuviškame vertime. Darbo uždaviniai: 1. Pateikti teorinę apžvalgą apie vertimą kaip mokslą. 2. Pristatyti lingvistinę medžiagą apie gramatines vertimo transformacijas, grupuojant jas į sukeitimas, praleidimas, pridėjimas, pakeitimas. 3. Paaiškinti grynų ir mišrių gramatinių transformacijų pasiskirstymą tyriamajameme kūrinyje. Darbo struktūra. Teorinėje dalyje daugiausia dėmesio skiriama vertimui. Aprašyti: vertimo studijų vystimasis, ekvivalentiškumas, vertimo metodai, procesai ir transformacijos. Praktinėje dalyje analizuojamas gramatinių vertimo transformacijų naudojimas remiantis surinktais pavyzdžiais.

The purpose of this paper is to discuss different translation strategies that may be used in translation from English to Swedish of a text on Country &amp; Western costuming. The focus will be on terminology, metaphors, and similes. In order to discuss the terminology, the metaphors, and simile, an English text has been translated into Swedish. To ensure a correct understanding of the source text, different dictionaries, encyclopaedias, various search engines and viewing services online have been very useful throughout the translation process. Corpora together with retailers’ web sites have also been valuable sources in providing variation and nuances to the translated text. Different sources on translation theory have also been reviewed; Newmark (1988) and Vinay and Darbelnet (1995). Terms have been selected out of their typical characteristic of being Western wear, and metaphors and simile out of their context to Western wear clothing. The results of the analysis show that a translator does not make use of one translation procedure when translating, but several. Which procedure that will be carried out is dependent on the context of the source text, the readership of the target text, the source text’s degree of specificity of the terminology, the source text’s imagery of the metaphors and simile, and the translator’s interpretation of the source text.

Machine translation offers the challenge of automatically translating a text from one natural language into another. Statistical methods - originating from the field of information theory - have shown to be a major breakthrough in the field of machine translation. Prior to this paradigm, many systems had been developed following a rule-based approach. This denotes a system based on a linguistic description of the languages involved and of how translation occurs in the mind of the (human) translator. Statistical models on the contrary use empirical means and may work with very little linguistic hypothesis on language and translation as performed by humans. This had implications for rule-based translation systems, in terms of software architecture and the nature of the rules, which were manually input and lack any statistical feature. In the view of such diverging paradigms, we can imagine trying to combine both in a hybrid system. In the present work, we start by examining the state-of-the-art of both rule-based and statistical systems. We restrict the rule-based approach to transfer-based systems. We compare rule-based and statistical paradigms in terms of global translation quality and give a qualitative analysis of their respective specific errors. We also introduce initial black-box hybrid models that confirm there is an expected gain in combining the two approaches. Motivated by the qualitative analysis, we focus our study and experiments on lexical phrasal rules. We propose a setup allowing to extract such resources from corpora. Going one step further in the integration of rule-based and statistical approaches, we then examine how to combine the extracted rules with decoding modules that will allow for a corpus-based handling of ambiguity. This then leads to the final delivery of this work: a rule-based system for which we can learn non-deterministic rules from corpora, and whose decoder can be optimised on a tuning set in the same domain.