The hydrophobic effect and hydrogen bonding interactions have long been considered to be the dominant forces in protein folding. However, the contribution of hydrogen bonds to stabilizing proteins has been difficult to clarify. As the intramolecular hydrogen bonds are formed in place of hydrogen bonds with solvent during folding, measures of stability fail to give a significant change in free energy. Previous studies on hydrogen bonding interactions have shown that they are only marginally important. Three long-range side chain-main chain hydrogen bonds have been found in the alpha subunit of tryptophan synthase (αTS), a (βα)8TIM barrel protein. These long-range noncovalent interactions connect either the N-terminus of one β-strand with the C-terminus of the succeeding and anti-parallel α-helix (F19-D46 and I97-D124) or the N-terminus of an α-helix with the C-terminus of the succeeding β-strand (A103-D130). By analogy, these interactions are designated as βα- or αβ-hairpin clamps. Surprisingly, the removal of any one of these clamp interactions, by replacement of the aspartic acid with alanine, results in significantly decreased thermodynamic stability for the native state and a substantial loss of secondary structure. When compared to several other side chain-side chain and short-range side chain-main chain interactions in αTS, these hairpin clamps clearly play a unique role in the structure and stability of αTS. The generality of these observations for βα-hairpin clamps in TIM barrel proteins was tested by experimental analysis of the clamps in a pair of homologous indole-3-glycerol phosphate synthase (IGPS) TIM barrels of low sequence identity. The results suggest that only the subset of conserved βα-hairpin clamps with hydrogen bond length less than 2.80 Å make substantive contributions to stability and/or structure. Those clamps with longer hydrogen bonds make modest contributions to stability and structure, similar to other types of side chain-main chain or side chain-side chain hydrogen bonds. The role of these clamps in defining the structures of the super-family of TIM barrel proteins was examined by a survey of 71 TIM barrel proteins from the structural database. Conserved features of βα-hairpin clamps are consistent with a 4-fold symmetry, with a predominance of main chain amide hydrogen bond donors near the N-terminus of the odd-number β-strands and side chain hydrogen bond acceptors in the loops between the subsequent α-helices and even-numbered β-strands. In this configuration, the clamps provide an N-terminal cap to odd-number β- strands in the β-barrel. Taken together, these findings suggest that βα-hairpin clamps are a vestigial signature of the fundamental βαβ building block for the (βα)8 motif and an integral part of the basic TIM barrel architecture. The relative paucity of βα-hairpin clamps remaining in TIM barrel structures and their variable contributions to stability imply that other determinants for structure and stability of the barrel have evolved to render a subset of the clamp interactions redundant. Distinct sequence preferences for the partners in the βα-hairpin clamps and the neighboring segments may be useful in enhancing algorithms for structure prediction and for engineering stability in TIM barrel proteins.

Notre recherche se situe dans le cadre du projet QWECI (Quantifying Weather and Climate Impacts on Health in Developing Countries, UE FP7) en partenariat avec l’UCAD, le CSE et l’IPD, autour de la thématique environnement-santé avec comme cas pratique les maladies à vecteurs au Sénégal et plus particulièrement la Fièvre de la Vallée du Rift (FVR). La santé des populations humaines et animales est souvent fortement influencée par l’environnement. D’ailleurs, la recherche sur les facteurs de propagation des maladies à transmission vectorielle, telle que la FVR, prend en compte cette problématique dans sa dimension aussi bien physique que socio-économique. Apparue en 1912-1913 au Kenya, la FVR est une anthropo-zoonose virale répandue dans les régions tropicales qui concerne principalement les animaux mais dont les hommes peuvent aussi être touchés. Au Sénégal, la zone à risque concerne en majorité la vallée du fleuve Sénégal et la zone sylvo-pastorale du Ferlo. Bien que de climat sahélien, le Ferlo regorge de nombreuses mares qui sont des sources d’approvisionnement en eau pour les hommes et le bétail mais également les gîtes larvaires pour les vecteurs potentiels de la FVR. La maîtrise de la FVR, carrefour de trois (03) grands systèmes (agro-écologique, pathogène, économique/sanitaire/social), implique nécessairement la prise en compte de plusieurs paramètres si l’on veut d’abord comprendre les mécanismes d’émergence mais aussi envisager le travail de modélisation du risque. Notre travail porte sur le processus décisionnel pour quantifier l’utilisation de données sanitaires et environnementales dans l’évaluation de leur impact pour le suivi de la FVR. Les équipes de recherche impliquées produisent des données lors de leurs enquêtes de terrains et des analyses de laboratoire. Ce flot de données croissant devrait être stocké et préparé à des études corrélées grâce aux nouvelles techniques de stockage que sont les entrepôts de données. A propos de l’analyse des données, il ne suffit pas de s’appuyer seulement sur les techniques classiques telles que les statistiques. En effet, la valeur ajoutée de contribution sur la question s’oriente vers une analyse prédictive combinant à la fois les techniques agrégées de stockage et des outils de traitement. Ainsi, pour la découverte d’informations, nouvelles et pertinentes à priori non évidentes, il est nécessaire de s’orienter vers la fouille de données. Par ailleurs, l’évolution de la maladie étant fortement liée à la dynamique spatio-temporelle environnementale des différents acteurs (vecteurs, virus et hôtes), cause pour laquelle nous nous appuyons sur les motifs spatio-temporels pour identifier et mesurer certaines interactions entre les paramètres environnementaux et les acteurs impliqués. Grâce au processus décisionnel, les résultats qui en découlent sont multiples :i. suivant la formalisation de la modélisation multidimensionnelle, nous avons construit un entrepôt de données intégré qui regroupe l’ensemble des objets qui participent à la gestion du risque sanitaire – ce modèle peut être généralisé aux maladies à vecteurs ;ii. malgré une très grande variété de moustiques, les Culex de type neavei et les Aedes de type ochraceus et vexans sont les vecteurs potentiels de la FVR les plus présents dans la zone d’étude et ce, durant la saison des pluies, période la plus sujette à des cas suspects ; la période à risque reste quand même le mois d’octobre ;iii. les mares analysées ont quasiment le même comportement, mais des variations significatives subsistent par endroits.Ce travail de recherche démontre une fois de plus l’intérêt pour la mise en évidence des relations entre les données environnementales et la FVR à partir de méthodes de fouille de données, pour la surveillance spatio-temporelle du risque d’émergence. / Our research is in part of the QWeCI european project (Quantifying Weather and Climate Impacts on Health in Developing Countries, EU FP7) in partnership with UCAD, the CSE and the IPD, around the theme of environmental health with the practical case on vector-borne diseases in Senegal and particularly the Valley Fever (RVF). The health of human and animal populations is often strongly influenced by the environment. Moreover, research on spread factors of vector-borne diseases such as RVF, considers this issue in its dimension both physical and socio-economic. Appeared in 1912-1913 in Kenya, RVF is a widespread viral anthropo-zoonosis in tropical regions which concerns animals but men can also be affected. In Senegal, the risk area concerns mainly the Senegal River Valley and the forestry-pastoral areas Ferlo. With a Sahelian climate, the Ferlo has several ponds that are sources of water supply for humans and livestock but also breeding sites for potential vectors of RVF. The controlling of the RVF, which is crossroads of three (03) large systems (agro-ecological, pathogen, economic/health/social), necessarily entails consideration of several parameters if one wants to first understand the mechanisms emergence but also consider the work on risk modeling. Our work focuses on the decision making process for quantify the use of health data and environmental data in the impact assessment for the monitoring of RVF. Research teams involved produce data during their investigations periods and laboratory analyzes. The growing flood of data should be stored and prepared for correlated studies with new storage techniques such as datawarehouses. About the data analysis, it is not enough to rely only on conventional techniques such as statistics. Indeed, the contribution on the issue is moving towards a predictive analysis combining both aggregate storage techniques and processing tools. Thus, to discover information, it is necessary to move towards datamining. Furthermore, the evolution of the disease is strongly linked to environmental spatio-temporal dynamics of different actors (vectors, viruses, and hosts), cause for which we rely on spatio-temporal patterns to identify and measure interactions between environmental parameters and the actors involved. With the decision-making process, we have obtained many results :i. following the formalization of multidimensional modeling, we have built an integrated datawarehouse that includes all the objects that are involved in managing the health risk - this model can be generalized to others vector-borne diseases;ii. despite a very wide variety of mosquitoes, Culex neavei, Aedes ochraceus and Aedes vexans are potential vectors of FVR. They are most present in the study area and, during the rainy season period which is most prone to suspected cases; the risk period still remains the month of October;iii. the analyzed ponds have almost the same behavior, but significant variations exist in some points.This research shows once again the interest in the discovery of relationships between environmental data and the FVR with datamining methods for the spatio-temporal monitoring of the risk of emergence.

Cette thèse propose l’introduction de scénarios temporels pour guider ou composer l’improvisation musicale homme-machine. Ce travail étudie la dialectique entre planification et réactivité dans les systèmes interactifs dédiés à l’improvisation : des systèmes informatiques pouvant générer de la musique en relation directe avec le contexte produit par une situation de concert. On cherche ici à appréhender l'improvisation pulsée et dite « idiomatique ». En s’appuyant sur l’existence d’une structure formalisée antérieure à la performance dans de nombreux répertoires improvisés (une « grille d’accords » par exemple) ces travaux proposent : un modèle d’improvisation guidée par un « scénario » introduisant des mécanismes d’anticipation ; une architecture temporelle hybride combinant anticipation et réactivité et permettant la synchronisation du rendu multimédia avec une pulsation non métronomique ; et un cadre pour composer des sessions d’improvisation idiomatique ou non à l’échelle du scénario en exploitant la généricité des modèles. Ces recherches ont été menées en interaction constante avec des musiciens experts, en intégrant pleinement ces collaborations au processus itératif de conception des modèles et architectures. Ceux-ci ont été implémentés dans le système ImproteK, utilisé à de nombreuses reprises lors de performances avec des improvisateurs. Au cours de ces collaborations, les sessions d'expérimentations ont été associées à des entretiens et séances de réécoute afin de recueillir de nombreuses appréciations formulées par les musiciens pour valider et affiner les choix technologiques. / This thesis focuses on the introduction of authoring and controls in human-computer music improvisation through the use of temporal scenarios to guide or compose interactive performances, and addresses the dialectic between planning and reactivity in interactive music systems dedicated to improvisation. An interactive system dedicated to music improvisation generates music on the fly, in relation to the musical context of a live performance. We focus here on pulsed and idiomatic music relying on a formalized and temporally structured object, for example a harmonic progression in jazz improvisation. The same way, the models and architecture we developed rely on a formal temporal structure. This thesis thus presents: a music generation model guided by a ''scenario'' introducing anticipatory behaviors; an architecture combining this anticipation with reactivity using mixed static/dynamic scheduling techniques; an audio rendering module to perform live re-injection of captured material in synchrony with a non-metronomic beat; and a framework to compose improvised interactive performances at the ''scenario'' level. This work fully integrated frequent interactions with expert musicians to the iterative design of the models and architectures. These latter are implemented in the interactive music system ImproteK that was used at various occasions during live performances with improvisers. During these collaborations, work sessions were associated to listening sessions and interviews to gather numerous judgments expressed by the musicians in order to validate and refine the scientific and technological choices.

High-throughput genomics projects have resulted in a rapid accumulation of protein sequences. Therefore, computational methods that can predict protein functions and functional sites efficiently and accurately are in high demand. In addition, prediction methods utilizing only sequence information are of particular interest because for most proteins, 3-dimensional structures are not available. However, there are several key challenges in developing methods for predicting protein function and functional sites. These challenges include the following: the construction of representative datasets to train and evaluate the method, the collection of features related to the protein functions, the selection of the most useful features, and the integration of selected features into suitable computational models. In this proposed study, we tackle these challenges by developing procedures for benchmark dataset construction and protein feature extraction, implementing efficient feature selection strategies, and developing effective machine learning algorithms for protein function and functional site predictions. We investigate these challenges in three bioinformatics tasks: the discovery of transmembrane beta-barrel (TMB) proteins in gram-negative bacterial proteomes, the identification of deleterious non-synonymous single nucleotide polymorphisms (nsSNPs), and the identification of helix-turn-helix (HTH) motifs from protein sequence.

No description available.

One of the most profound open questions in biology is how the genetic code developed. The blueprints for proteins are encoded by triplets of nucleic acids, which in turn require proteins for interpretation and replication. The mere existence of this self-referencing system is a chicken-and-egg dilemma. Aminoacyl-tRNA synthetases are key players in the transfer of genetic information and reflect the earliest episode of life. These enzymes are responsible for loading tRNA molecules with the correct amino acid. Two protein superfamilies of aminoacyl-tRNA synthetases emerged, each responsible for ten amino acids. Despite sequence and structure similarity, the delicate balance between these superfamilies is manifested in two structural motifs, which were identified in the context of this thesis: the Backbone Brackets and the Arginine Tweezers. Both motifs realize constant ligand recognition and can be found in almost all protein structures of aminoacyl-tRNA synthetases. In this thesis, I thoroughly characterized Backbone Brackets and Arginine Tweezers. The specific characteristics of these motifs require high-precision methods for their detection and analysis. However, existing algorithms do not feature an adequate computational representation of structural motifs at the atom level and the support of isofunctional residue mutations. In order to address these limitations, I designed the Fit3D algorithm for template-based and template-free detection of structural motifs. I show that proper computational representation of structural motifs is crucial and improves accuracy up to 26% for a benchmark dataset. Fit3D is a general-purpose tool for structural motif detection in high-resolution protein structure data. In conjunction with the accelerating progress in experimental methods, the demand for such tools will increase rapidly over the next years. I applied Fit3D to structures of aminoacyl-tRNA synthetases to investigate whether Backbone Brackets and Arginine Tweezers are universal building blocks for ligand recognition, and to quantify structural changes upon ligand binding. While the Arginine Tweezers motif is exclusively found in aminoacyl-tRNA synthetases and paralogs, the Backbone Brackets seem to be a general pattern to recognize functional groups of certain ligands. The results show subtle differences in side chain orientation for one structural motif and a backbone shift for the other. This suggests a structural rearrangement to be a general mechanism in some aminoacyl-tRNA synthetases. The detailed level of these analyses would not have been possible without high-precision structural motif detection with Fit3D. The results emphasize the importance of structural motifs, which consist of only a few residues, for the global function of the enzyme. Furthermore, the stunning conservation of the structural motifs located in the core domains of aminoacyl-tRNA synthetases suggests their presence in the earliest predecessors of these enzymes. Both motifs might have played a fundamental role in shaping the genetic code as we know it.

Peter L. Berger's conception of agency in his earliest writings (c.1954-1960) is logically and empirically inadequate. At the root of this inadequacy is an idealism that prevents him from providing a compelling account of actual empirical agency. Chapter 1 asserts that Berger's earlier works warrant analysis. Chapter 2 discusses Berger's earliest influences, particularly Max Weber and The Swedish Lund School of motif research. Chapter 3 identifies a unique commitment to Christian Humanism at the base of Berger's conception of agency. Chapter 4 clarifies how Berger's Christian humanism interacts with his Weberian, and Parsonian-inspired functional analysis of the American religious establishment. The thesis concludes (Chapter 5) by identifying more specifically how and why Berger's Christian humanism undermines his attempt to empirically ground human agency.

Pharmaceutical solids tend to exist in different physical forms termed as polymorphs. Issues about pharmaceutical systems are mainly concerned with the active ingredient's physico-chemical stability and bioavailability. The main aim of this study is to investigate the non-bonded interactions in pharmaceutical solids that govern the physical pharmaceutics performance of such materials and through the use of structural techniques and correlation of these results with crystal structural database to establish the presence of physical motifs in selected systems. Structural motifs were identified by the use of single crystal and crystal packing analysis on diverse range of pharma-relevant materials including chalcones, cryptolepines, biguanides and xanthines. These selected systems were validated using functional group and molecular analysis and correlating them to the Cambridge Structural Database. Crystallization studies are done on these selected systems as well as exploiting those using synthetic analogues. A total of 51 crystal structures were investigated including 16 new structure determinations. Addition synthesis of new xanthines to investigate novel intermolecular patterns was also undertaken. The understanding and exploitation of intermolecular interactions involving hydrogen bonds and coordination complexation during packing can be used in the design and synthesis of solid state molecular structures with desired physical and chemical properties.

Both technological and experimental advancements in the field of biotechnology have allowed scientists to make leaps in areas such nucleic acid, antibody, and recombinant protein technologies. Here we focus on the use of recombinant proteins as molecular recognition motifs, wound healing biomaterials, and agents for cell cycle pathway elucidation are discussed. The author's primary project is described in chapters 2 and 3, and is focused on designed leucine-rich repeat proteins which offer increased stability, modularity, and surface area for binding interactions. These proteins bind at least two muramyl dipeptide ligands with picomolar to nanomolar affinity (Kd1 = 0.04 – 3.5 nM); as measured by fluorescence quenching experiments and ITC. The longest designed repeat, CLRR8, has a Kd app value of 1.0 nM which is comparable to full length native NOD2 protein. Molecular docking simulations revealed the locations of two potential binding sites and their respective interactions. The series of proteins represents a foundation for a high affinity and highly specific molecular recognition scaffold that has the potential to bind a variety of ligands. Previously the author contributed to the design of recombinant keratin proteins, and the work in Chapter 4 builds on the original design to allow for controlled degradation in wound healing systems. Site-directed mutagenesis was utilized to introduce these degradation sites, and modified keratin proteins were expressed with no differences to native recombinant keratin proteins. Success in engineering a variation of native keratin protein with no issues in expression lay the foundation for further engineering of native keratin or other relevant proteins for improved functionality. Chapter 5 describes steps towards producing human Aurora borealis (Bora) protein, an important substrate in cell cycle regulation, by in vitro transcription-translation with locked Ser–Pro analogues. This will allow for the elucidation of the active isomerization form to ensure proper cell division. Site-directed mutagenesis successfully introduced the amber codon to relevant Ser-Pro sites at positions 274 and 278. These mutated Bora genes along with modified ribosomes and aminoacyl tRNA will allow for the incorporation of locked dipeptide analogues. Expression of native Bora was carried out as a control, and appeared to express in dimeric form. The experiments carried out in Chapter 5 describe and outline all the molecular biology work completed and to be completed for this novel method of studying cis-trans isomerization in living cells. / Doctor of Philosophy / Sequencing of the human genome and the rapid development of gene editing and recombinant DNA technologies paved the way for a massive shift in the pharmaceutical industry. The first pharmaceutical companies in the 19th century started as fine chemicals businesses. The discovery of penicillin introduced antibiotics, and improved synthetic techniques led to the giants we know as big pharma today. Today, in the 21st century both computing and biotechnology has allowed for great leaps forward in precision medicine. Biotechnology refers to the manipulation of living organisms or their components to produce useful commercial products. In the pharmaceutical industry this refers to genetic engineering for novel pharmaceuticals. Here, we focus on the use of recombinant technology to create proteins for use in biomedical applications. Recombinant proteins are proteins formed by laboratory methods of molecular cloning. Through this technology, we are able to elucidate sequence-structure-function relationships of proteins, and determine their specific functions. Additionally, recombinant methods allow us to fine tune or modify the sequences of natural proteins to be more effective scaffolds or reagents. Chapter 3 focuses on the development of synthetic proteins for medical diagnostics. We designed a protein scaffold, based on natural innate immunity proteins, to detect bacteria cell wall components. Chapter 4 focuses on the engineering of keratin protein with applications in wound healing. We introduce controlled degradation of the biomaterial for use in potential drug delivery systems at the wound site. Chapter 5 focuses on the use of recombinant technologies aiding in the elucidation of a regulatory protein's function in cell division.

Cette thèse cherche à cerner, dans Malicroix d’Henri Bosco, le cheminement qui préside à l’écriture du récit lui-même. Dans ce dessein, nous utilisons une approche poïétique qui s’intéresse à « l’œuvre en train de se faire », selon l’expression de René Passeron. Nous considérons ainsi l’œuvre comme une poétique d’auteur sous forme fictionnelle. La perspective phénoménologique que nous adoptons permet d’étudier le texte sous l’angle de la perception, alors que la mythocritique offre un point de vue privilégié pour réfléchir la perception du monde – particulièrement le monde textuel – par le biais du sacré et de son imagerie. Reconstruisant pas à pas la double structure – horizontale et verticale – du récit, nous nous penchons sur divers aspects de l’œuvre et du processus scriptural. L’horizon de lecture forme le premier chapitre de notre thèse et donne lieu à une vue triple sur le récit : l’histoire et les personnages, le contexte spatio-temporel et le point de vue du mythe comprenant le mythe fondateur du récit et le scénario initiatique qui en découle. Nous regroupons dans le deuxième chapitre l’élaboration de deux notions qui fondent notre étude poïétique, soient les figures et les chronotopes. Les figures consistent en deux groupes, les figures de l’écrivain et celles de l’expression qui jouent des rôles distincts dans le cheminement scriptural et s’inscrivent dans Malicroix par le biais des personnages. L’étude des chronotopes divise le récit en onze temps-espace qui constituent la trame d’un cheminement des figures suivant le parcours du texte. Le troisième chapitre détaille cette traversée des chronotopes qu’effectuent les figures, dessinant le chemin de l’écriture dans le texte selon onze situations successives. Le dernier chapitre de cette étude comporte deux parties. La première met en lumière une poétique d’écrivain bosquienne comme l’auteur la formule dans un bref article intitulé « L’exaltation et l’amplitude ». La seconde, le point d’arrivée de notre étude, intègre les données de la poétique d’écrivain au cheminement des onze situations, fournissant une description des étapes du processus scriptural que suit Bosco en écrivant Malicroix. / This thesis schematizes, in Malicroix by Henri Bosco, the process that presides to the writing of the novel itself. Using a poietic approach, we consider the text as a writer’s poetic that takes a fictional form. A phenomenological perspective allows us to study the novel from the point of view of perception, and mythocritique enables us to reflect on the perception of the world – especially the world of the text – through the angle of the sacred and its symbols. Reconstructing the horizontal and vertical structures of the novel, we reflect on diverse aspects of the text and of the scriptural process. The reading horizon constitutes the first chapter of our thesis and offers a triple view on the novel: the story and the characters, the spatiotemporal context and the mythical point of view. In the second chapter are elaborated two central notions, the figures and the chronotopes. Two groups of figures emerge, one associated with the writer as creator of the text and the other, with the process of expression. The figures play distinct roles in the conception and expression and are represented in Malicroix by way of the characters. The chronotopes study divides the novel in eleven times-spaces that constitute the basis of the figures’ progression through the text. The third chapter details how the figures cross the chronotopes’ series, drawing the scriptural route inscribed in eleven successive situations in the text. The last chapter contains two parts. The first examines the writer’s poetic that Bosco published under the title « L’exaltation et l’amplitude ». The second, which constitutes the final objective of our study, integrates the elements of this writer’s poetic in the eleven successive situations, producing a description of the stages of the scriptural process followed by Bosco while writing Malicroix.