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<p>In prokaryotes, several mRNA sequences surrounding the initiation codon have been found to influence the translation process; these include the downstream region and its codon context, the Shine-Dalgarno sequence and the S1 ribosomal protein-binding site. In this thesis, the purpose has been to study the role of the downstream region and Shine-Dalgarno-like sequences on early translation elongation and gene expression in <i>Escherichia coli</i>.</p><p>The downstream region (DR) after the initiation codon (around five to seven codons), has an important role in the initiation of translation. We find that most of the codons which give very low gene expression at +2 (considering AUG as +1), reach 5 to 10 fold higher expression when those codons are positioned posteriori to +2, with the exception of the NGG codons. The NGG codons abort the translation process if located within the first five codons of the DR, due to peptidyl-tRNA drop-off. However, when the NGG codons are situated further down from the DR, the protein expression was increased at the same level of expression as in the presence of any other codon.</p><p>The Shine-Dalgarno (SD) is an important region of initiation in translation of bacteria. In spite of this, it has been found that Gram-negative bacteria could translate mRNAs with weak or non-functional SD, while the DR carries out a main role in the efficiency of translation. In addition, positions of SD and SD-like sequences are very important to direct initiation of translation in the choice between two possible initiation codons. A strong SD between two initiation sites will favor the second initiation site if it consists of a canonical start codon followed by a good DR.</p><p>The results suggest that the mRNA sequences surrounding the initiation codon: the downstream region and the Shine-Dalgarno and SD-like sequences, are very important contributors to the translation level and gene expression in <i>Escherichia coli</i>.</p>

In prokaryotes, several mRNA sequences surrounding the initiation codon have been found to influence the translation process; these include the downstream region and its codon context, the Shine-Dalgarno sequence and the S1 ribosomal protein-binding site. In this thesis, the purpose has been to study the role of the downstream region and Shine-Dalgarno-like sequences on early translation elongation and gene expression in Escherichia coli. The downstream region (DR) after the initiation codon (around five to seven codons), has an important role in the initiation of translation. We find that most of the codons which give very low gene expression at +2 (considering AUG as +1), reach 5 to 10 fold higher expression when those codons are positioned posteriori to +2, with the exception of the NGG codons. The NGG codons abort the translation process if located within the first five codons of the DR, due to peptidyl-tRNA drop-off. However, when the NGG codons are situated further down from the DR, the protein expression was increased at the same level of expression as in the presence of any other codon. The Shine-Dalgarno (SD) is an important region of initiation in translation of bacteria. In spite of this, it has been found that Gram-negative bacteria could translate mRNAs with weak or non-functional SD, while the DR carries out a main role in the efficiency of translation. In addition, positions of SD and SD-like sequences are very important to direct initiation of translation in the choice between two possible initiation codons. A strong SD between two initiation sites will favor the second initiation site if it consists of a canonical start codon followed by a good DR. The results suggest that the mRNA sequences surrounding the initiation codon: the downstream region and the Shine-Dalgarno and SD-like sequences, are very important contributors to the translation level and gene expression in Escherichia coli.

Computational Insights into Intergenic Regions and Overlapping Genes among Prokaryote GenomesTot i la gran varietat d'estils de vida de les espècies bacterianes, tots ells presenten trets arquitectònics comuns. En aquesta tesi s'estudia les regions intergèniques i els solapaments entre gens en els genomes procariotes.Hem vist que per predir els orígens de replicació, a part de l'anàlisi de la composició de nucleòtids del DNA, es requereix experiments computacionals complementaris per aconseguir millors prediccions. Els solapaments entre gens acostumen a ser curts, respecten el codi genètic i es veuen influenciats per la pressió selectiva en contra de grans solapaments. En canvi, com més llarg és un solapament entre dos gens, més risc hi ha que una mutació pugui afectar a dues proteïnes de la cèl·lula al mateix temps. Hem detectat que els solapaments més llargs de 60 parells de bases són deguts a errors en la seqüenciació o en l'anotació dels gens. En quant a les regions intergèniques, hem vist que la presència d'una seqüència reguladora entre gens, com és la Shine-Dalgarno (responsable de iniciar eficientment la traducció de RNA missatger a proteïna) pot influir en la mida d'aquestes regions i afectar l'ús de codons d'aturada. Finalment, hem construït una aplicació web ( http://genomes.urv.cat/pwneigh/ ) que permet estudiar fàcilment la conservació els solapaments en les espècies i les regions intergèniques en els genomes procariotes. / Computational Insights into Intergenic Regions and Overlapping Genes among Prokaryote GenomesAlthough prokaryote organisms live in a huge variety of habitats, they have architectural features in common. In this thesis we analyze the intergenic regions and the overlaps between genes among the prokaryote genomes.Although the DNA compositional analysis brings us near to the origin of replication, alternative analyses are required in order to achieve better predictions. The overlaps between prokaryote genes tend to be short and they arise according to the structure of the genetic code. Furthermore, there is a selective pressure against the long ones. As longer is an overlap there is more risk of a deleterious mutation that can affect two proteins of the cell. We detected that the overlaps longer than 60 bps are due to sequencing or annotation errors. Regarding the intergenic regions we found that the presence of a regulatory signal such as the Shine-Dalgarno sequence (responsible of an efficient translation of the mRNA to protein) can influence the length of this regions and the stop codon usage of the previous genes. Finally, we developed the PairWise Neighbours database ( http://genomes.urv.cat/pwneigh/ ) which permits the study of the overlaps and its conservation across the species, as well as the SD presence within the intergenic regions.Albert Pallejà CaroDepartament de Bioquímica i BiotecnologiaUniversitat Rovira i VirgiliCampus Sesceladesc/Marcel·lí Domingo, s/n43007 Tarragona - Catalunya

Ce travail de recherche analyse le concept du sublime dans l’esthétique hégélienne à partir des sources les plus directes à disposition : les leçons berlinoises sur la philosophie de l’art, à travers les Nachschriften ou cahiers de notes des élèves de Hegel. Ainsi, ce travail s’inscrit dans une position critique vis-à-vis de l’édition de ces leçons faite par H. G. Hotho. L’analyse se démarque de ladite lecture phénoménologique et s’efforce de montrer la nécessité d’une lecture logique de l’esthétique hégélienne en exposant la dialectique interne de cette esthétique, qui opère comme un devenir logico-esthétique des catégories de la Science de la logique. Plus particulièrement, l’objectif de cette thèse est de mettre en évidence l’existence d’une correspondance entre la catégorie esthétique du sublime et la catégorie logique du Schein ou « apparence » telle qu’exposée dans La doctrine de l’essence. Finalement, nous nous proposons ici de démontrer que le sublime compris comme Schein doit être mis en lien avec la catégorie fondamentale de cette esthétique, à savoir l’idéal, qui à son tour, à partir de cette correspondance avec les catégories de la logique de l’essence, est montré comme le moment de l’Erscheinung ou « apparition » de l’idée. Cette réflexion propose ainsi une détermination plus cohérente de l’idéal que la définition canonique contestée et cherche à mettre en avant une réponse à ce qui est considéré comme la question centrale de cette philosophie de l’art, à savoir la possibilité de la conciliation entre les deux aspects de l’œuvre d’art : l’esprit absolu comme contenu spirituel et la figure sensible comme son expression. / This research work is an analysis of the concept of the sublime within the Hegelian aesthetic, based on the most direct sources of available Berlin lectures on philosophy of art - i.e. the Nachschriften or notebooks from Hegel’s students. Therefore, it adopts a critical point of view regarding the edition of these lectures made by H. G. Hotho.This work distinguishes itself from the so-called phenomenological reading and aims to demonstrate the need of a logical way of reading the Hegelian aesthetic and presenting its inner dialectic, which develops as a logical and aesthetic evolution of the categories in the Science of Logic. Particularly, this thesis’ objective consists in revealing the existence of a connection between the aesthetic category of the sublime and the logical category of Schein or “shine”, as presented in the “Doctrine of the essence.” Finally, it is also proposed that the sublime, understood as Schein, should be correlated with the fundamental category of this aesthetic: namely the ideal, which in turn is shown as the moment of Erscheinung or “appearance” of the idea, based on the connection with the categories of the essence of logic. This suggests a more consistent determination of the ideal compared to the disputed canonical definition, and is intended to give an answer to a question that is considered the main issue of this philosophy of art: how is it possible to accomplish a balance between the two subjects of the artwork - the absolute spirit as spiritual content and the sensitive form as its expression.

The evaluation of the gloss of human hair, following wet/dry chemical treatments such as bleaching, dyeing and perming, has received much scientific and commercial attention. Current gloss analysis techniques use constrained viewing conditions where the hair tresses are observed under directional lighting, within a calibrated presentation environment. The hair tresses are classified by applying computational models of the fibres' physical and optical attributes and evaluated by either a panel of human observers, or the computational modelling of gloss intensity distributions processed from captured digital images. The most popular technique used in industry for automatically assessing hair gloss is to digitally capture images of the hair tresses and produce a classification based upon the average gloss intensity distribution. Unfortunately, the results from current computational modelling techniques are often found to be inconsistent when compared to the panel discriminations of human observers. In order to develop a Gloss Evaluation System that produces the same judgements as those produced from both computational models and human psychophysical panel assessments, the human visual system has to be considered. An image based Gloss Evaluation System with gonio-capture capability has been developed, characterised and tested. A new interpretation of the interaction between reflection bands has been identified on the hair tress images and a novel method was developed to segment the diffuse, chroma and specular regions from the image of the hair tress. A new model has been developed, based on Hunter's contrast gloss approach, to quantify the gloss of the human hair tress. Furthermore, a large number of hair tresses have been treated with a range of hair products to simulate different levels of hair shine. The Tresses have been treated with different commercial products. To conduct a psychophysical experiment, one-dimensional scaling paired comparison test, a MATLAB GUI (Graphical user interface) was developed to display images of the hair tress on calibrated screen. Participants were asked to select the image that demonstrated the greatest gloss. To understand what users were attending to and how they used the different reflection bands in their quantification of the gloss of the human hair tress, the GUI was run on an Eye-Tracking System. The results of several gloss evaluation models were compared with the participants' choices from the psychophysical experiment. The novel gloss assessment models developed during this research correlated more closely with the participants' choices and were more sensitive to changes in gloss than the conventional models used in the study.

L’étonnement a une place privilégiée dans la vie des idées, considéré comme l’émotion à l’origine de toutes formes de spéculations philosophiques, il est l’objet d’étude le plus adéquat pour analyser les problèmes communs du cinéma et de la philosophie : le mouvement (Thalès, Héraclite, Zénon d’Élée), la remise en question du réel (Descartes), l’accès au savoir par les sens (Platon). Par l’incarnation de « personnages conceptuels » (l’idiot, le sceptique, le jeune philosophe), le cinéma offre la possibilité d’accéder à des raisonnements philosophiques de manière empirique. Le cinéma sera ainsi considéré comme un outil pouvant mettre en scène le doute cartésien grâce à une déconstruction progressive du réel. Chaque film étudié matérialisera une étape de cette déconstruction : Three Days of the Condor de Sydney Pollack : la remise en question du réel ; Aguirre, la colère de Dieu de Werner Herzog et Bullitt de Peter Yates : le déni du réel, la filmographie de Buster Keaton (courts et longs-métrages) : la trahison des apparences, les œuvres abstraites de Stan Brakhage : la réduction du réel à un entrelacement de formes et de sensations. Cette thèse proposera une redéfinition des causes et des conditions du surgissement de l’étonnement. En effet, étant principalement lié au nouveau dans les différents traités sur l’émotion étudiés (Descartes, Darwin, Charles Le Brun, William James), le rapport entre étonnement et mémoire nécessitera un développement. Ainsi par l’intermédiaire d’une revalorisation de la mémoire affective dans la perception d’un objet étonnant, cette émotion pourra enfin être prise en compte en fonction du passé du sujet. Les différents types de reconnaissance engagés dans la vision d’un film seront analysés pour comprendre à quel moment ce phénomène passe d’un événement mineur à un événement majeur. Le cinéma pourra de cette manière être employé comme un laboratoire mémoriel. Grâce à une approche anthropologique de la première cause de l'étonnement au cinéma : "les feuilles qui bougent" c’est-à-dire le mouvement, le mythe des images vivantes sera étudié du point de vue de sa persistance à différents moments de l’histoire du cinéma du Napoléon d’Abel Gance à Young Sherlock Holmes de Barry Levinson. Ce premier principe étonnant du dispositif cinématographique donnera lieu à une inversion, 4 l’étonnement suscité par une autre vie des images cette fois insufflée par la suspension ou l’arrêt sur image. Enfin « le phénomène saturé » défini par Jean-Luc Marion comme un étonnement surplombant le champ de vision du spectateur sera divisé en une typologie des différents types de saturation au cinéma (le réel surpris, le montage cubiste, la plénitude du cadre etc.), dans le but de trouver un équivalent visuel de l'évidence (première obsession cartésienne). Le dessein de cette typologie inspirée par Descartes sera de réhabiliser les sens dans la construction du savoir / Astonishment has a privileged place in the history of philosophy, considered as the emotion behind all forms of philosophical speculation; it is the most appropriate object of study to analyze the common problems of cinema and Philosophy: movement (Thales, Heraclitus, Zeno of Elea), questioning reality (Descartes), access to knowledge through the senses (Plato). Cinema will thus be considered as a tool able to portray Cartesian doubt through a progressive deconstruction of reality. Each film studied materializes a stage of this deconstruction: Three Days of the Condor by Sydney Pollack: questioning reality Aguirre, the Wrath of God by Werner Herzog and Bullitt by Peter Yates: the denial of reality the filmography of Buster Keaton (short and feature films); the betrayal of appearances the abstract works of Stan Brakhage: the reduction of reality to an interweaving of forms and sensations. Thus, by the incarnation of « conceptual characters » (the idiot, the skeptic, the young philosopher), cinema allows us to empirically access to philosophical reasoning. This development will also involve the redefinition of the causes and conditions of astonishment. Indeed, the relationship between astonishment and memory will necessitate a further investigation into, since it is mainly linked to the new and the extraordinary in the different treatises on emotion studied (Descartes, Darwin, Charles Le Brun, William James). Thus, by means of a revaluation of the affective memory in the perception of an astonishing object, this emotion can finally be considered according to the past of the subject. The different types of recognition involved in filmic vision will be analyzed to understand when this phenomenon moves from being a minor event to a major event. In this way, cinema can be used as a memorial laboratory. Thanks to an anthropological approach to the primary cause of astonishment in the cinema: « the moving leaves » (i.e. movement), the myth of living images, will be studied through its persistence at different moments of cinema history from Abel Gance’s Napoleon to Young Sherlock Holmes by Barry Levinson. The first principle of cinematic astonishment leads us to consider its inversion, the astonishment aroused by another aspect of life of images, one dominated by the suspension or the halting of the image. Finally, the « Saturated Phenomena » (defined by Jean-Luc Marion as an astonishment overlooking the spectator's field of vision) will be divided into a typology of the different 6 types of saturation in the cinema (cubist montage, crowded frames, etc.) in order to find a visual equivalent of the evidence (the first Cartesian obsession) and to reassert the value of the senses in the construction of knowledge