My work uses process as a course of action that marks the death of moments through a continuous stream of consciousness. I metaphorically link disparate pieces of information to the human condition in order to present multiple readings through juxtaposition. I assemble both abstract and figurative subject matter in a collage-like manner through methods of cropping and fragmentation to symbolize the disjuncture I feel is indicative of how we experience the world through short-lived thoughts, feelings, and actions.

My work uses process as a course of action that marks the death of moments through a continuous stream of consciousness. I metaphorically link disparate pieces of information to the human condition in order to present multiple readings through juxtaposition. I assemble both abstract and figurative subject matter in a collage-like manner through methods of cropping and fragmentation to symbolize the disjuncture I feel is indicative of how we experience the world through short-lived thoughts, feelings, and actions.

Microsatellites are repetitive DNA characterized by tandem repeats of short motifs (2 – 5 bp). High mutation rates make them ideal for population level studies. Microsatellite allele genesis is generally attributed to strand slippage, and it is assumed that alleles are caused only by changes in repeat number. Most analyses are limited to alleles (electromorphs) scored by mobility only, and models of evolution rarely account for homoplasy in allele length. Additionally, insertion/deletion events (indels) in the flanking region or interruptions in the repeat can obfuscate the accuracy of genotyping. Many investigators use microsatellites, designed for a focal species, to screen for genetic variation in non-focal species. Comparative studies have shown different mutation rates of microsatellites in different species, and even individuals. Recent studies have used reciprocal comparisons to assess the level of polymorphism of microsatellites between pairs of taxa. In this study, I investigated the evolution of microsatellites within a phylogenetic context, using comparisons within the rodent family Bathyergidae. Bathyergidae represents a monophyletic group endemic to sub-Saharan Africa and relationships are well supported by morphological and molecular data. Using mitochondrial and nuclear DNA, a robust phylogeny was generated for the Bathyergidae. From my results, I proposed the new genus, Coetomys. I designed species-specific genotyping and microsatellite flanking sequence (MFS) primers for each genus. Sequencing of the MFS provided direct evidence of the evolutionary dynamics of the repeat motifs and their flanking sequence, including rampant electromorphic homoplasy, null alleles, and indels. This adds to the growing body of evidence regarding problems with genotype scores from fragment analysis. A number of the loci isolated were linked with repetitive elements (LTRs and SINEs), characterized as robust phylogenetic characters. Results suggest that cryptic variation in microsatellite loci are not trivial and should be assessed in all studies. The phylogenetic utility of the nucleotide variation of the MFS was compared to the well-resolved relationships of this family based on the 12S/TTR phylogeny. Variation observed in MFS generated robust phylogenies, congruent with results from 12S/TTR. Finally, a number of the indels within the MFS provided a suite of suitable phylogenetic characters.

Websites are shifting from static model to dynamic model, in order to deliver their users with dynamic, interactive, and personalized experiences. However, dynamic content generation comes at a cost – each request requires computation as well as communication across multiple components within the website and across the Internet. In fact, dynamic pages are constructed on the fly, on demand. Due to their construction overheads and non-cacheability, dynamic pages result in substantially increased user response times, server load and increased bandwidth consumption, as compared to static pages. With the exponential growth of Internet traffic and with websites becoming increasingly complex, performance and scalability have become major bottlenecks for dynamic websites. A variety of strategies have been proposed to address these issues. Many of these solutions perform well in their individual contexts, but have not been analyzed in an integrated fashion. In our work, we have carried out a study of combining a carefully chosen set of these approaches and analyzed their behavior. Specifically, we consider solutions based on the recently-proposed fragment caching technique, since it ensures both correctness and freshness of page contents. We have developed mechanisms for reducing bandwidth consumption and dynamic page construction overheads by integrating fragment caching with various techniques such as proxy-based caching of dynamic contents, pre-generating pages, and caching program code. We start with presenting a dynamic proxy caching technique that combines the benefits of both proxy-based and server-side caching approaches, without suffering from their individual limitations. This technique concentrates on reducing the bandwidth consumption due to dynamic web pages. Then, we move on to presenting mechanisms for reducing dynamic page construction times -- during normal loading, this is done through a hybrid technique of fragment caching and page pre-generation, utilizing the excess capacity with which web servers are typically provisioned to handle peak loads. During peak loading, this is achieved by integrating fragment-caching and code-caching, optionally augmented with page pre-generation. In summary, we present a variety of methods for integrating existing solutions for serving dynamic web pages with the goal of achieving reduced bandwidth consumption from the web infrastructure perspective, and reduced page construction times from user perspective.

Les sélénoprotéines sont des protéines auxquelles des sélénocystéines, soit le 21e acide aminé, sont incorporées durant leur traduction. Plus précisément, la sélénocystéine (Sec) est un dérivé métabolique de la sérine, mais structurellement équivalent à une cystéine dont on a remplacé l'atome de soufre par du sélénium. Elle se distingue des autres acides aminés puisqu’elle possède sa propre synthétase qui sert à convertir la sérine en Sec alors que le résidu est déjà fixé à l’ARNt. La position d’une Sec sur l’ARNm est indiquée par le codon UGA étant habituellement un signal STOP introduisant le concept de recoding. Grâce à une machinerie métabolique spécifique à l'ARNtSec et à la présence d’un SecIS (Selenocystein Insertion Sequence) sur l’ARNm, ce codon permet la présence d'une Sec dans la protéine. Il est connu que la synthèse débute avec l’acétylation de l’ARNt[Ser]Sec par la seryl-ARNt synthétase (SerRS) afin de donner la seryl-ARNt[Ser]Sec. Cette dernière est subséquemment phosphorylée par l’O-phosphoséryl-ARNt[Ser]Sec kinase (PSTK) qui donnera l’O-phosphoséryl-ARNt[Ser]Sec. Par la suite, un complexe de plusieurs protéines et cofacteurs, agissant comme machinerie pour l’incorporation des Sec durant la traduction, s’associe avec l’ARNt[Ser]Sec puis l’ARNm et, finalement, les composantes du ribosome. Parmi ces protéines, SepSecS catalyse l’étape finale de la synthèse des Sec en convertissant le O-phosphoseryl-ARNt[Ser]Sec en selenocysteinyl-ARNt[Ser]Sec utilisant le sélénophosphate comme source de sélénium. Des études récentes montrent que l’association avec SECp43 serait nécessaire pour que SepSecS joue son rôle et soit ségrégée au noyau pour s’associer à la machinerie de biosynthèse des sélénoprotéines, soit le complexe moléculaire qui reconnaît le codon UGA. Parmi les protéines de la machinerie de biosynthèse des sélénoprotéines que nous avons analysées, il y a eEFSec, RPL30, SPS2, SPS1, SBP2 et NSEP1. Nos résultats d’analyse de la dynamique de l’interaction entre les constituants de la machinerie de biosynthèse et d’incorporation des Sec, confirment plusieurs données de la littérature, mais remettent en question le modèle jusqu’à maintenant établi. Une meilleure compréhension de la dynamique des interactions entre ses constituants et la régulation de cette dynamique permet d’émettre des hypothèses quant au rôle de la machinerie de biosynthèse des sélénoprotéines et de l’importance de sa complexité. Nous avons analysé les interactions in vivo dans des cellules HEK293T au moyen de la technique de Protein-Fragment Complementation Assay (PCA) en couplant, par un clonage moléculaire, les gènes de chacune des protéines d’intérêt avec des fragments des gènes de la protéine luciférase (hRluc). Nous avons ainsi réalisé une fusion en N-terminal et en C-terminal des fragments de luciférase pour chacune des protéines d’intérêt. Puis, nous avons analysé la dynamique des interactions avec les composantes de la machinerie de biosynthèse des Sec. D’autres travaux seront essentiels afin de bâtir sur les résultats présentés dans cette recherche. / Selenoproteins are proteins that incorporate selenocysteines, which is called the 21st amino acid, during their translation. Specifically, selenocysteine (Sec) is a metabolic derivate of serine, which is structurally equivalent to Cys except for replacement of sulfur with an atom of selenium in the δ-position. It differs from other amino acids since a unique synthetase converts the serine into Sec while the residue is already attached to the tRNA. The codon for Sec on the mRNA is a UGA codon that is usually a STOP signal, introducing the concept of "recoding". Through a specific metabolic machinery for the tRNASec and the presence of a SecIS (Selenocysteine Insertion Sequence) on the mRNA, this codon allows the incorporation of the Sec into the protein. However, the mechanism of biosynthesis of this amino acid and its incorporation into proteins is not well understood. It is known that the synthesis starts with the acetylation of tRNA[Ser]Sec by seryl-tRNA synthetase (SerRS) to give the seryl-tRNA[Ser]Sec. The latter is subsequently phosphorylated by the O-phosphoseryl-tRNA[Ser]Sec kinase (PSTK) which will generate the O-phosphoseryl-tRNA[Ser]Sec. Subsequently, a large complex of several proteins and cofactors acting as machinery for incorporation of Sec during translation, associates with tRNA[Ser]Sec and the mRNA and finally, the components of the ribosome. Among these proteins, SepSecS catalyzes the final step in the biosynthesis of Sec converting O-phosphoseryl-tRNA[Ser]Sec into selenocysteinyl-tRNA[Ser]Sec using monoselenophosphate as a source of selenium. Recent studies showed that the association with SECp43 would be required for SepSecS to play its role to segregate into the nucleus to be associated with the machinery that recognizes the UGA codon. Among the proteins of the biosynthesis machinery of selenoproteins that we analyzed, there are eEFSec, RPL30, SPS2, SPS1, SBP2 and NSEP1. Results of analysis of the dynamics of the interaction between the components of the Sec biosynthetic machinery confirm some data from the literature, but conflict with the model so far established. A better understanding of the dynamics of interactions between its constituents and the reaction of this process would allow us to make assumptions about the role of the biosynthetic machinery of selenoproteins and the importance of its complexity. We analyzed the dynamics of interaction in vivo in HEK293T cells using a Protein-Fragment Complementation Assay (PCA) based on a humanized Renilla luciferase (hRLuc) by coupling, by molecular cloning, genes encoding each protein of interest with gene encoding fragments of the luciferase protein (hRluc). We have thus achieved an expression of fusion of N-terminal and C-terminal fragments for each luciferase protein of interest. Then, we analyzed the dynamics of the interaction with the components of the Sec biosynthetic machinery. Further work will be essential to build on the results presented in this research.

Le triméthoprime (TMP) est un antibiotique communément utilisé depuis les années 60. Le TMP est un inhibiteur de la dihydrofolate réductase (DHFR) bactérienne chromosomale. Cette enzyme est responsable de la réduction du dihydrofolate (DHF) en tétrahydrofolate (THF) chez les bactéries, qui lui, est essentiel à la synthèse des purines et ainsi, à la prolifération cellulaire. La résistance bactérienne au TMP est documentée depuis plus de 30 ans. Une des causes de cette résistance provient du fait que certaines souches bactériennes expriment une DHFR plasmidique, la DHFR R67. La DHFR R67 n'est pas affectée par le TMP, et peut ainsi remplacer la DHFR chromosomale lorsque celle-ci est inhibée par le TMP. À ce jour, aucun inhibiteur spécifique de la DHFR R67 est connu. En découvrant des inhibiteurs contre la DHFR R67, il serait possible de lever la résistance au TMP que la DHFR R67 confère aux bactéries. Afin de découvrir des inhibiteurs de DHFR R67, les approches de design à base de fragments et de criblage virtuel ont été choisies. L'approche de design à base de fragments a permis d'identifier sept composés simples et de faible poids moléculaire (fragments) inhibant faiblement la DHFR R67. À partir de ces fragments, des composés plus complexes et symétriques, inhibant la DHFR R67 dans l'ordre du micromolaire, ont été élaborés. Des études cinétiques ont montré que ces inhibiteurs sont compétitifs et qu'au moins deux molécules se lient simultanément dans le site actif de la DHFR R67. L'étude d'analogues des inhibiteurs micromolaires de la DHFR R67 a permis de déterminer que la présence de groupements carboxylate, benzimidazole et que la longueur des molécules influencent la puissance des inhibiteurs. Une étude par arrimage moléculaire, appuyée par les résultats in vitro, a permis d'élaborer un modèle qui suggère que les résidus Lys32, Gln67 et Ile68 seraient impliqués dans la liaison avec les inhibiteurs. Le criblage virtuel de la librairie de 80 000 composés de Maybridge avec le logiciel Moldock, et les essais d'inhibition in vitro des meilleurs candidats, a permis d'identifier quatre inhibiteurs micromolaires appartenant à des familles distinctes des composés précédemment identifiés. Un second criblage virtuel, d'une banque de 6 millions de composés, a permis d'identifier trois inhibiteurs micromolaires toujours distincts. Ces résultats offrent la base à partir de laquelle il sera possible de développer iv des composés plus efficaces et possédant des propriétés phamacologiquement acceptables dans le but de développer un antibiotique pouvant lever la résistance au TMP conféré par la DHFR R67. / Trimethoprim (TMP) is a common antibiotic which is used since the 60's. TMP is an inhibitor of the bacterial chromosomal dihydrofolate reductase (DHFR). This enzyme catalyses the reduction of the dihydrofolate (DHF) to tetrahydrofolate (THF) which is essential to the biosynthesis of purines thus to cellular proliferation. Bacterial TMP resistance is documented since about 30 years. One of the cause of this resistance comes from the fact that certain bacteria express a plasmidic DHFR, the R67 DHFR, which confers TMP resistance. The R67 DHFR is not inhibited by TMP and can replace the chromosomal DHFR when the latter is inhibited by TMP. The discovery of R67 DHFR inhibitors would allow to break the trimethoprim resistance granted by R67 DHFR. In order to discover R67 DHFR inhibitors, fragment based design and virtual screening approaches were selected. By fragment based design, seven simple compounds with a low molecular mass which inhibited weakly R67 DHFR (fragments) were identified. From these fragments, more complex and symmetrical compounds inhibiting R67 DHFR in the micromolar range were identified. Kinetic studies showed these inhibitors were competitive and at least two molecules bind simultaneously to the active site of the R67 DHFR. Test of the micromolar inhibitors analog showed that the presence of carboxylate, benzimidazole and the length of the molecule all have an effect on the potency of the inhibitors. Molecular docking of the inhibitors, supported by in vitro data, were used to develop a model which suggest that residue like Lys32, Gln67 and Ile68 would be involved in the binding of the inhibitors to the R67 DHFR. Virtual screening of the 80 000 compound Maybridge library with Moldock software, followed by in vitro test of the best candidate, identified four micromolar inhibitors which are chemically distinct from the inhibitor beforehand identified. A second virtual screening of a 6 million compounds bank identified three micromolar inhibitors which are also distinct from the inhibitor beforehand identified. vi These results offer a basis which will allow further development of more potent inhibitors with more acceptable pharmacologic properties in order to develop an antibiotic which would break the TMP resistance granted by the R67 DHFR.

Cette thèse a pour but de développer le pendant in silico des étapes clés du Fragment-Based Drug Design (FBDD), et ce dans le cadre plus général du développement de l'outil S4MPLE. Le FBDD génère des ligands drug-like à partir de petites molécules (fragments). Après une étape de validation de S4MPLE et de sa fonction d'énergie, un recentrage autour du FBDD est réalisé, à travers le docking puis l'optimisation virtuelle de fragments par growing ou linking (G/L). Cette stratégie reposesur 1) la création d'une chimiothèque focalisée en connectant un ou deux fragment(s) avec des linkers pré-générés, et 2) l'échantillonnage avec S4MPLE des composés chimères dans le site avec des contraintes. Des simulations de G/L plus ou moins ambitieuses (site flexible, ajout de H2O libres) permettent de valider cette approche avec des études rétrospectives basées sur des données expérimentales. La dernière phase de la thèse a consisté à appliquer ce protocole in silico à un projet de l'entreprise.

The increased use of digital media to store legal, as well as illegal data, has created the need for specialized tools that can monitor, control and even recover this data. An important task in computer forensics and security is to identify the true le type to which a computer le or computer le fragment belongs. File type identi cation is traditionally done by means of metadata, such as le extensions and le header and footer signatures. As a result, traditional metadata-based le object type identi cation techniques work well in cases where the required metadata is available and unaltered. However, traditional approaches are not reliable when the integrity of metadata is not guaranteed or metadata is unavailable. As an alternative, any pattern in the content of a le object can be used to determine the associated le type. This is called content-based le object type identi cation. Supervised learning techniques can be used to infer a le object type classi er by exploiting some unique pattern that underlies a le type's common le structure. This study builds on existing literature regarding the use of supervised learning techniques for content-based le object type identi cation, and explores the combined use of multilayer perceptron neural network classi ers and linear programming-based discriminant classi ers as a solution to the multiple class le fragment type identi cation problem. The purpose of this study was to investigate and compare the use of a single multilayer perceptron neural network classi er, a single linear programming-based discriminant classi- er and a combined ensemble of these classi ers in the eld of le type identi cation. The ability of each individual classi er and the ensemble of these classi ers to accurately predict the le type to which a le fragment belongs were tested empirically. The study found that both a multilayer perceptron neural network and a linear programming- based discriminant classi er (used in a round robin) seemed to perform well in solving the multiple class le fragment type identi cation problem. The results of combining multilayer perceptron neural network classi ers and linear programming-based discriminant classi ers in an ensemble were not better than those of the single optimized classi ers. / MSc (Computer Science), North-West University, Potchefstroom Campus, 2013

The increased use of digital media to store legal, as well as illegal data, has created the need for specialized tools that can monitor, control and even recover this data. An important task in computer forensics and security is to identify the true le type to which a computer le or computer le fragment belongs. File type identi cation is traditionally done by means of metadata, such as le extensions and le header and footer signatures. As a result, traditional metadata-based le object type identi cation techniques work well in cases where the required metadata is available and unaltered. However, traditional approaches are not reliable when the integrity of metadata is not guaranteed or metadata is unavailable. As an alternative, any pattern in the content of a le object can be used to determine the associated le type. This is called content-based le object type identi cation. Supervised learning techniques can be used to infer a le object type classi er by exploiting some unique pattern that underlies a le type's common le structure. This study builds on existing literature regarding the use of supervised learning techniques for content-based le object type identi cation, and explores the combined use of multilayer perceptron neural network classi ers and linear programming-based discriminant classi ers as a solution to the multiple class le fragment type identi cation problem. The purpose of this study was to investigate and compare the use of a single multilayer perceptron neural network classi er, a single linear programming-based discriminant classi- er and a combined ensemble of these classi ers in the eld of le type identi cation. The ability of each individual classi er and the ensemble of these classi ers to accurately predict the le type to which a le fragment belongs were tested empirically. The study found that both a multilayer perceptron neural network and a linear programming- based discriminant classi er (used in a round robin) seemed to perform well in solving the multiple class le fragment type identi cation problem. The results of combining multilayer perceptron neural network classi ers and linear programming-based discriminant classi ers in an ensemble were not better than those of the single optimized classi ers. / MSc (Computer Science), North-West University, Potchefstroom Campus, 2013

While the study of complete sources is very valuable, and has contributed greatly to what is understood of music history, the perspective they contribute is limited because they cannot reveal information about how music and music sources were most often used. The study of functional sources, more probably created for use, allows for more insight into how music was performed and understood, and how such sources were created, used and valued. This study examines twelve fragmentary early sixteenth-century English sources from the Digital Image Archive of Medieval Music (DIAMM) database, constituting a sample of functional music sources in this period. The study of this sampling reveals information about how functional manuscripts were created, used and valued in England during this time period. Some of the fragments contain works with concordances. These concordances are compared using variant comparison, where differences in the versions of the work are considered and weighed. The comparative study of concordances provides insight into the transmission of the versions, scribal and performance culture, as well as into music culture in general. Overall, the study of this sampling of early sixteenth-century functional English sources provides a clearer understanding of the use of accidentals, scribes and scribal culture, performers, performance practice and music culture in England at this time, contributing to the understanding of music history.