Thesis advisor: Michelle M. Meyer / Thesis advisor: Peter Clote / Structured RNAs have many biological functions ranging from catalysis of chemical reactions to gene regulation. Many of these homologous structured RNAs display most of their conservation at the secondary or tertiary structure level. As a result, strategies for natural structured RNA discovery rely heavily on identification of sequences sharing a common stable secondary structure. However, correctly identifying the functional elements of the structure continues to be challenging. In addition to studying natural RNAs, we improve our ability to distinguish functional elements by studying sequences derived from in vitro selection experiments to select structured RNAs that bind specific proteins. In this thesis, we seek to improve methods for distinguishing functional RNA structures from arbitrarily predicted structures in sequencing data. To do so, we developed novel algorithms that prioritize the structural properties of the RNA that are under selection. In order to identify natural structured ncRNAs, we bring concepts from evolutionary biology to bear on the de novo RNA discovery process. Since there is selective pressure to maintain the structure, we apply molecular evolution concepts such as neutrality to identify functional RNA structures. We hypothesize that alignments corresponding to structured RNAs should consist of neutral sequences. During the course of this work, we developed a novel measure of neutrality, the structure ensemble neutrality (SEN), which calculates neutrality by averaging the magnitude of structure retained over all single point mutations to a given sequence. In order to analyze in vitro selection data for RNA-protein binding motifs, we developed a novel framework that identifies enriched substructures in the sequence pool. Our method accounts for both sequence and structure components by abstracting the overall secondary structure into smaller substructures composed of a single base-pair stack. Unlike many current tools, our algorithm is designed to deal with the large data sets coming from high-throughput sequencing. In conclusion, our algorithms have similar performance to existing programs. However, unlike previous methods, our algorithms are designed to leverage the evolutionary selective pressures in order to emphasize functional structure conservation. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Title: Multiple sequence alignment using genetic algorithms Author: Zdeněk Pátek Department: Department of Software and Computer Science Education Supervisor: RNDr. František Mráz, CSc. Abstract: The thesis adresses the problem of multiple sequence alignment (MSA). It contains the specication of the proposed method MSAMS that allows to find motifs in biological sequences, to split sequences to blocks using the motifs, to solve MSA on the blocks and nally to assemble the global alignment from the aligned blocks and motifs. Motif search and MSA are both solved using genetic algorithms. The thesis describes the implementation of the method, conguration of its settings, benchmarking on the BAliBASE database and comparison to the ClustalW program. Experimental results showed that MSAMS can discover better alignments than ClustalW. Keywords: multiple sequence alignment, motif nding, genetic algorithms, ClustalW

In recent time particular interest has been drawn to the inference of gene regulatory networks from microarray gene expression data. But despite major improvements with data based methods, the network reconstruction from expression data alone still presents a computationally complex (NP-hard) problem. In this work it is incorporated additional information – regulatory motifs from yeast, when inferring a gene regulatory network for mouse genes. It was put forward the hypothesis that regulatory patterns analogous to these motifs are present in the set of mouse genes and can be identified by comparing yeast and mouse genes in terms of sequence similarity or Gene Ontology (The Gene Ontology Consortium 2000) annotations. In order to examine this hypothesis, small permutations of genes with high similarity to such yeast gene regulatory motifs were first tested against simple data-driven regulatory networks by means of consistency with the expression data. And secondly, using the best scored interactions provided by these permutations it were then inferred networks for the whole set of mouse genes. The results showed that individual permutations of genes with a high similarity to a given yeast motif did not perform better than low scored motifs and that complete networks, which were inferred from regulatory interactions provided by permutations, did also neither show any noticeable improvement over the corresponding data-driven network nor a high consistency with the expression data at all. It was therefore found that the hypothesis failed, i.e. neither the use of sequence similarity nor searching for identical functional annotations between mouse and yeast genes allowed to identify sets of genes that showed a high consistency with the expression data or would have allowed for an improved gene regulatory network inference.

<p>In recent time particular interest has been drawn to the inference of gene regulatory networks from microarray gene expression data. But despite major improvements with data based methods, the network reconstruction from expression data alone still presents a computationally complex (NP-hard) problem. In this work it is incorporated additional information – regulatory motifs from yeast, when inferring a gene regulatory network for mouse genes. It was put forward the hypothesis that regulatory patterns analogous to these motifs are present in the set of mouse genes and can be identified by comparing yeast and mouse genes in terms of sequence similarity or Gene Ontology (The Gene Ontology Consortium 2000) annotations.</p><p>In order to examine this hypothesis, small permutations of genes with high similarity to such yeast gene regulatory motifs were first tested against simple data-driven regulatory networks by means of consistency with the expression data. And secondly, using the best scored interactions provided by these permutations it were then inferred networks for the whole set of mouse genes.</p><p>The results showed that individual permutations of genes with a high similarity to a given yeast motif did not perform better than low scored motifs and that complete networks, which were inferred from regulatory interactions provided by permutations, did also neither show any noticeable improvement over the corresponding data-driven network nor a high consistency with the expression data at all.</p><p>It was therefore found that the hypothesis failed, i.e. neither the use of sequence similarity nor searching for identical functional annotations between mouse and yeast genes allowed to identify sets of genes that showed a high consistency with the expression data or would have allowed for an improved gene regulatory network inference.</p>

Made available in DSpace on 2014-06-12T16:01:15Z (GMT). No. of bitstreams: 2 arquivo7278_1.pdf: 2063761 bytes, checksum: eaeb6780fe875052548e747b8a3af1a9 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2005 / A regulação gênica está intimamente ligada com a transcrição de proteínas, e esse mecanismo é muito importante para o desenvolvimento dos seres vivos, pois é através dele que os organismos conseguem sintetizar proteínas. Um interessante problema da biologia moderna é o entendimento de mecanismos da regulação da transcrição. Muitos aspectos dessa regulação envolvem fatores de transcrição (proteínas ligantes ao DNA). Esses fatores regulam a expressão gênica pela conexão em posições específicas de regiões do genoma (conjunto de genes de uma espécie) que podem estar próximas ou não, como veremos em maiores detalhes oportunamente. Os fatores de transcrição conectam-se a subseqüências especificas de DNA, os promotores, que podem, com dificuldade, ser determinados por análises biológicas. Esse alto grau de dificuldade motiva os cientistas a procurarem meios computacionais mais rápidos e eficientes para solucionar o problema da busca pelos sítios de ligação dos promotores. O crescente aumento da disponibilidade de seqüências completas de genoma motiva tentativas de entender e modelar o mecanismo regulatório através de análises computacionais. A identificação de sítios de ligação envolve duas etapas principais: aprender modelos de sítios de ligação e buscar sítios em novas seqüências. Parte do trabalho foi desenvolver uma ferramenta para auxiliar os cientistas na busca por essas regiões especiais, os motifs, no genoma. Como desenvolvemos essa ferramenta usando Java, combinamos o fonema inglês da letra "J" com o sufixo "nom" da palavra "genom" para compor o nome da ferramenta e a chamamos de Jnom. A primeira tarefa é aprender modelos de sítios de ligação em potencial em um dado genoma. Usam-se exemplos de sítios de ligação verificados biologicamente e tenta-se encontrar sítios similares em outras regiões promotoras. Em seguida, é necessário descobrir uma seqüência de motifs em uma coleção de longas seqüências que são supostamente ligadas pelo mesmo fator. Neste caso, um motif encontrado indica um possível fator desconhecido que regula o conjunto de genes. A natureza combinatória dos fatores de transcrição é o mecanismo pelo qual as células dos seres superiores (eucariotes) atuam para controlar a expressão de conjuntos inteiros de genes. A intenção deste trabalho é investigar essa natureza combinante e tentar utilizar esse fato para melhorar o desempenho em relação a ferramentas existentes. O principal objetivo dessa pesquisa é construir uma ferramenta capaz de considerar a ação combinada dos fatores de transcrição através da seqüência de genes para encontrar novos motifs a partir de alguns já conhecidos

L’intérêt des composés organiques fluorés est de nos jours de plus en plus important en raison de leur large domaine d’application. Par exemple, dans le domaine de la chimie médicinale, la présence d’un atome de fluor altère sensiblement les propriétés physicochimiques des molécules et permet très souvent une amélioration de leur profil thérapeutique.Dans ce contexte, notre laboratoire s’intéresse au développement de nouveaux fluoropeptidomimétiques dans le but de pallier les différents problèmes associés aux peptides (pauvre biodisponibilité, flexibilité conformationnelle). Parmi les différents peptidomimétiques connus, le motif fluorooléfine (CF=CH) peut être considéré comme unisostère de la liaison peptidique du à ses similarités stériques et électroniques.Dans le but de proposer un mode d’accès général aux pseudopeptides fluorés comportant une fluorooléfine à la place du lien peptidique, nous avons développé une nouvelle stratégie basée sur une étape d’addition nucléophile de réactifs organométalliques sur des N-(tertbutanesulfinyl)-a-fluoroénimines chirales. Cette méthodologie nous permet de contrôler le centre asymétrique du côté N-terminal du peptide.Nous avons ensuite appliqué cette stratégie à la synthèse de composés biologiquement actifs tels que le 26RFa, un neuropeptide impliqué dans le contrôle et la régulation de la prise alimentaire. Dans ce contexte, plusieurs dipeptides fluorés ont été synthétisés puis incorporés au sein de l’heptapeptide qui ont donné lieu à des études de relations structureactivité. / Fluoroorganic compounds are increasingly popular owing to their wide range of biological applications. For example, in the field of medicinal chemistry, fluorinated molecules clearlyalter physicochemical properties compared to non-fluorinated derivatives, and often with animproved therapeutic profile.In this context, our laboratory is interested in the development of new fluoropeptidomimetics aiming at circumventing common problems associated with peptides(poor bioavaibility, flexibility). For this purpose, the fluoroolefin moiety (CF=CH) can act as aneffective peptide bond mimic due to steric and electronic similarities.In our project aiming at proposing general synthesis methods of fluorinated pseudopeptides featuring a fluoroolefin moiety as the peptide bond analogue, we develop a new strategy based on nucleophilic addition of organometallic reagents to chiral N-(tert-butanesulfinyl)-a-fluoroenimines. This methodology allows us to control the asymmetric center on the Nterminalside of the peptide.Then, we applied our strategy to the synthesis of biologically active compound such as the26RFa, a neuropeptide involved in regulation and food intake. In this context, several fluorinated dipeptides have been synthesized and incorporated into the natural heptapeptide for a structure-activity relationship study.

Anti-Semitism, or Jew hatred, much of which is expressed and communicated through folklore, has a long history and continues unabated today. Incendiary opinions, deadly misconceptions, and insidious accusations have plagued Jews throughout history. Anti-Semitic expressions and incidents are scattered throughout countless texts, but no single comprehensive reference work that compiles all forms of anti-Semitic folklore motifs exists. This thesis attempts to fill that gap by supplying an index of anti-Semitic motifs. To establish a baseline of already catalogued anti-Semitic motifs, all six volumes of Stith Thompson's Motif-Index of Folklore-Literature: A Classification of Narrative Elements in Folktales, Ballads, Myths, Fables, Mediaeval Romances, Exempla, Fabliaux, Jest-Books and Local Legends were scanned and any relevant motifs listed were archived in a card index. Approximately 250 more previously unidentified motifs were documented from historical materials, published books and articles, artifacts, and personal communications. All motifs used in this study were developed from English sources, or from English speakers borrowing from other languages and cultures. The procedure to categorize the folklore motifs is based on a numbering system developed by folklorist Stith Thompson in 1955. Using Thompson's classifications of motifs as a base, the approximately 250 newly identified anti-Semitic folklore motifs I discovered have been integrated with Thompson motifs. Anti-Semitic materials covered begin with the Middle Ages and continue to the present day. Although not comprehensive, this motif index incorporates examples of anti-Semitic folklore from all genres, making motifs and examples easily accessible for anyone who wishes to analyze historical and current anti-Semitism. Indexing anti-Semitic folklore in a single reference work based on a universal folklore indexing system creates a body of information to be used as a resource tool for education and research of anti-Semitism. Furthermore, the index can easily be expanded as more material comes to light.

Comprendre le câblage complexe de la régulation cellulaire reste un défi des plus redoutables.Les connaissances fondamentales sur le câblage et le fonctionnement du réseau d’homéostasiedes protéines aideront à mieux comprendre comment l’homéostasie des protéines échouedans les maladies et comment les modèles de régulation du réseau d’homéostasie desprotéines peuvent être ciblés pour une intervention thérapeutique. L’étude vise à développeret à appliquer une nouvelle méthodologie de calcul pour l’identification systématique etla caractérisation des systèmes de rétroaction en homéostasie des protéines. La rechercheproposée combine des idées et des approches issues de la science des protéines, de la biologiedes systèmes de levure, de la biologie computationnelle et de la biologie des réseaux.La difficulté dans la tâche d’incorporer des données multi-plateformes multi-omiques estamplifiée par le vaste réseau de gènes, protéines et métabolites interconnectés qui seréunissent pour remplir une fonction spécifique. Pour ma thèse de maîtrise, j’ai développéun algorithme PBPF (Path-Based Pattern Finding), qui recherche et énumère les motifsde réseau de la topologie requise. Il s’agit d’un algorithme basé sur la théorie des graphesqui utilise la combinaison d’une méthode transversale de profondeur et d’une méthodede recherche par largeur ensuite pour identifier les topologies de sous-graphes de réseaurequises. En outre, le fonctionnement de l’algorithme a été démontré dans les domainesde l’homéostasie des protéines chezSaccharomyces cerevisiae. Une approche systématiqued’intégration des données de la biologie des systèmes a été orchestrée, qui montre l’iden-tification systématique de motifs de rétroaction régulatrice connus dans l’homéostasie desprotéines. Il revendique fortement la capacité d’identifier de nouveaux motifs de rétroactionréglementaire envahissants. L’application de l’algorithme peut être étendue à d’autressystèmes biologiques, par exemple, pour identifier des motifs de rétroaction spécifiques àl’état cellulaire dans le cas de cellules souches. / Understanding the intricate wiring of cellular regulation remains a most formidable chal-lenge. The fundamental insights into the wiring and functioning of the protein homeostasisnetwork will help to better understand how protein homeostasis fails in diseases and howthe regulatory patterns of protein homeostasis network can be targeted for therapeuticintervention. The study aims at developing and applying novel computational methodologyfor the systematic identification and characterization of feedback systems in proteinhomeostasis. The proposed research combines ideas and approaches from protein science,yeast systems biology, computational biology, as well as network biology. The difficultyin the task of incorporating multi-platform multi-omics data is amplified by the largenetwork of inter-connected genes, proteins and metabolites that come together to perform aspecific function. For my master’s thesis, I developed a path-based pattern finding (PBPF)algorithm, which searches and enumerates network motifs of required topology. It is a graphtheory based algorithm which utilizes the combination of depth-first transverse method andbreadth-first search method to identify the required network sub-graph topologies. Further,the functioning of the algorithm has been demonstrated in the realms of protein homeostasisinSaccharomyces cerevisiae. A systematic approach of integration of systems biologydata has been orchestrated, which shows the systematic identification of known regulatoryfeedback motifs in protein homeostasis. It claims the unique ability to identify novelpervasive regulatory feedback motifs. The application of the algorithm can be extended toother biological systems, for example, to identify cell-state specific feedback motifs in caseof stem-cells.

Les variétés de Picard sont des variétés de Shimura associées au groupe des similitudes unitaires d'un espace hermitien de dimension 3 sur un corps CM. Elles paramétrisent les classes d'isomorphismes de variétés abdéliennes munies de certaines structures supplémentaires. En particulier, il existe une variété abdélienne universelle sur une variété de Picard et plus généralement des familles de Kuga-Sato.A ces variétés sont attachés des groupes de cohomologie. L'un des intérêts de telles variétés est qu'il est possible de trouver des représentations automorphes dans les groupes de cohomologie qui lui sont attachés, en particulier dans les groupes de cohomologie intérieure. Selon le programme de Langlands, ces représentations correspondent conjecturalement à des motifs. Le résultat principal de cette thèse est la construction de facteurs directs du motif intérieur de certaines familles de Kuga-Sato sur des variétés de Picard, c'est-a-dire d'un analogue motivique de la cohomologie intérieure. Cela passe par une étude détaillée des poids du motif bord de ces familles. On en déduit l'existence de motifs associés à certaines représentations automorphes. / Picard varieties are Shimura varieties associated to the group of unitary similitudes of an hermitian space of dimension 3 over a CM eld. They parametrize isomorphism classes of abelian varieties with some additional data. In particular, there exists a universal abelian variety over a Picard variety and more generally Kuga-Sato families. Cohomology groups are attached to these varieties. Automorphic representations can be found in cohomology groups, more precisely in interior cohomology groups. Following Langlands' program, these representations correspond conjecturally to motives. The main result of this thesis is the construction of direct factors of the interior motive of certain Kuga-Sato families over a Picard variety, meaning a motivic analogue of interior cohomology. To prove this, we study the weights of the boundary motive of such families. We deduce from this the existence of a motive associated to certain automorphic representations.

L’un des obstacles majeurs au développement de nouveaux antipaludiques est notre connaissance limitée de la biologie parasitaire et la rareté des cibles thérapeutiques potentielles identifiées. Les interactions protéines-protéines sont impliquées et essentielles dans divers processus biologiques incluant les modifications post-traductionnelles. Les interactions substrats-kinases ou phosphatases sont considérées comme une liaison transitoire et jouent un rôle central et essentiel dans le cycle cellulaire de Plasmodium. La Ser/Thr Protéine Phosphatase de Type 1 (PP1), l’une des phosphatases majeurs des eucaryotes, est essentielle à la survie du parasite Plasmodium falciparum, responsable du paludisme. Elle est régulée par diverses sous-unités régulatrices dont plus de 200 ont été identifiées chez l’Homme, mais seulement 4 chez Plasmodium.Afin d’explorer le réseau de régulation de la P. falciparum PP1 (PfPP1), nous avons utilisé trois approches complémentaires pour caractériser l’interactome de la PfPP1. La purification par co-affinité suivie d'une analyse par spectrométrie de masse a identifié 6 protéines interagissant avec la PfPP1 dont 3 contenaient le motif consensus d’interaction RVxF, 2 autres le motif Fxx[RK]x[RK], également connu pour interagir avec la phosphatase et une protéine avec les deux motifs de liaison. Le criblage par double hybride chez la levure a identifié 134 protéines dont 30 présentent le motif RVxF et 20 ont le motif de liaison Fxx[RK]x[RK]. Le criblage in silico du génome de P. falciparum en utilisant une séquence consensus du motif RVxF a révélé 55 partenaires potentiels de la PfPP1. Afin de confirmer l’interaction de certaines protéines, 35 partenaires candidats ont été validés par un test d’interaction de type ELISA. Les résultats ont permis de détecter aussi bien des partenaires conservés de la PP1 qu'un nombre élevé d'interacteurs spécifiques à la PP1 du parasite et montrent une grande diversité dans les fonctions biologiques impliquant la PP1 chez Plasmodium. Parmi ces candidats, un partenaire appelé Gametocyte EXported Protein 15 (GEXP15) a été confirmé comme un réel partenaire de la PfPP1 par différentes approches. De plus, GEXP15 est surexprimé chez les gamétocytes, stade responsable de la transmission du parasite chez le moustique. Ces résultats ainsi que des études fonctionnelles seront présentés. / A major obstacle in the development of novel anti-malarials is our limited knowledge of basic parasite biology and the paucity of identified potential intervention targets. Protein-protein interactions are involved and essential in broad range of biological processes including the post-translational modifications. Substrate-kinase or phosphatase interactions are considered as transient binding and play a central and essential role in Plasmodium cell cycle. The Ser/Thr Protein Phosphatase Type 1 (PP1), one of the main contributors of eukaryotic phosphatase activity, is essential to malaria parasite Plasmodium falciparum and is highly regulated by many regulatory subunits. In humans, there are about 200 distinct regulators, however, only 4 have been so far reported in Plasmodium.To explore the P. falciparum PP1 (PfPP1) regulatory network as complete as possible, we carried out three complementary approaches to characterize the PfPP1 interactome. Co-affinity purification followed by Mass Spectrometry-based proteomics identified 6 PfPP1 interacting proteins (PIPs) of which 3 contained the RVxF consensus binding motif, 2 PIPs with a Fxx[RK]x[RK] binding motif, one with both binding motifs. The Yeast Two-Hybrid screening identified 134 proteins of which 30 have the RVxF binding motif and 20 contain the Fxx[RK]x[RK] binding motif. The in silico screen of the P. falciparum genome using a consensus RVxF motif as template revealed the presence of 55 potential PfPP1 interacting proteins. As further demonstration, 35 candidate partners were validated in an independent ELISA-based assay using recombinant proteins. The data reports several conserved PP1 interacting proteins as well as a high number of specific interactors to PfPP1, indicating a high diversity of biological functions for PP1 in Plasmodium. Among these candidates, one partner assigned as Gametocyte EXported Protein 15 (GEXP15) has been confirmed as a direct interactor of PfPP1 by different approaches. In addition, GEXP15 is over-expressed during gametocyte stage, responsible for the transmission of the parasite in the mosquito. These results as well as functional studies will be presented and discussed.