Understanding the mechanism of recombination has important implications for genome evolution and genomic variability. The work presented in this thesis studies the properties of recombination by investigating the effects it has on genome evolution in humans and dogs. Using alignments of human genes with chimpanzee and macaque orthologues we studied substitution patterns along the human lineage and scanned for evidence of positive selection. The properties mirror the situation in human non-coding sequences with the fixation bias ‘GC-biased gene conversion’ (gBGC) as a driving force in the most rapidly evolving regions. By assigning candidate genes to distinct classes of evolutionary forces we quantified the extent of those genes affected by gBGC to 20%. This suggests that human-specific characters can be prompted by the fixation bias of gBGC, which can be mistaken for selection. The gene PRDM9 controls recombination in most mammals, but is lacking in dogs. Using whole-genome alignments of dog with related species we examined the effects of PRDM9 inactivation. Additionally, we analyzed genomic variation in the genomes of several dog breeds. We identified that non-allelic homologous recombination (NAHR) via sequence identity, often GC-rich, creates structural variants of genomic regions. We show that these regions, which are also found in dog recombination hotspots, are a subset of unmethylated CpG-islands (CGIs). We inferred that CGIs have experienced a drastic increase in biased substitution rates, concurrent with a shift of recombination to target these regions. This enables recurrent episodes of gBGC to shape their distribution. The work presented in this thesis demonstrates the importance of meiotic recombination on patterns of molecular evolution and genomic variability in humans and dogs. Bioinformatic analyses identified mechanisms that regulate genome composition. gBGC is presented as an alternative to positive selection and is revealed as a major factor affecting allele configuration and the emergence of accelerated evolution on the human lineage. Characterization of recombination-induced sequence patterns highlights the potential of non-methylation and establishes unmethylated CGIs as targets of meiotic recombination in dogs. These observations describe recombination as an interesting process in genome evolution and provide further insights into the mechanisms of genomic variability.

Master of Engineering / This thesis presents an innovative human promoter recognition model HPR-PCA. Principal component analysis (PCA) is applied on context feature selection DNA sequences and the prediction network is built with the artificial neural network (ANN). A thorough literature review of all the relevant topics in the promoter prediction field is also provided. As the main technique of HPR-PCA, the application of PCA on feature selection is firstly developed. In order to find informative and discriminative features for effective classification, PCA is applied on the different n-mer promoter and exon combined frequency matrices, and principal components (PCs) of each matrix are generated to construct the new feature space. ANN built classifiers are used to test the discriminability of each feature space. Finally, the 3 and 5-mer feature matrix is selected as the context feature in this model. Two proposed schemes of HPR-PCA model are discussed and the implementations of sub-modules in each scheme are introduced. The context features selected by PCA are III used to build three promoter and non-promoter classifiers. CpG-island modules are embedded into models in different ways. In the comparison, Scheme I obtains better prediction results on two test sets so it is adopted as the model for HPR-PCA for further evaluation. Three existing promoter prediction systems are used to compare to HPR-PCA on three test sets including the chromosome 22 sequence. The performance of HPR-PCA is outstanding compared to the other four systems.

It has long been established that the spinal cord is able to produce locomotor activity on its own. Despite extensive research identifying and describing the involvement of multiple spinal neuron populations that are part of the spinal locomotor circuit, the manner in which these different components act together to precisely control the rhythm and the pattern of activation of muscles during locomotion remains largely undetermined. We sought to shed light on how the components of spinal locomotor circuits interact to produce robust locomotion using a developmental approach in zebrafish larvae. We used electrophysiological techniques to observe how the rhythm generation mechanism developed while the fish was transitioning from an early form of swimming to a more mature swimming behaviour. In the process we were able to highlight fundamental changes in the organization of spinal locomotor circuits as its operation moves from a pacemaker-based architecture relying on intrinsic properties of neurons to a network oscillator-based architecture relying on synaptic connectivity to generate proper rhythm driving the fish tail beats. Additionally, we revealed that this transition occurred at different times along the spinal cord progressing in a caudorostral direction. By combining these experimental observations with already published insights we were able to propose models of spinal locomotor circuits reproducing the successive locomotor behaviours encountered through development. By incrementing supplementing the circuit model in a manner that reflected biological processes by which the nervous system maturates (neurogenesis, synaptic connectivity refinement and maturation of intrinsic properties) we mirrored the natural development of the spinal locomotor circuit. This series of successively constructed models permitted us to pinpoint possible roles of specific neural populations for swimming behaviour as well as eventual targets and mechanism of actions of neuromodulators (serotonin and dopamine). In the process, I further provided testable hypotheses for future inquiries. Overall, the experimental findings in combination with the modeling work are an important step forward in fully understanding how the spinal cord generates swimming movements in zebrafish.

Made available in DSpace on 2015-06-17T19:34:33Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-08-04. Added 1 bitstream(s) on 2015-06-18T12:48:38Z : No. of bitstreams: 1 000828456_20160101.pdf: 422063 bytes, checksum: 8476834ceb55ae5bce2c637566dd5def (MD5) Bitstreams deleted on 2016-01-04T10:26:22Z: 000828456_20160101.pdf,. Added 1 bitstream(s) on 2016-01-04T10:28:15Z : No. of bitstreams: 1 000828456.pdf: 2122241 bytes, checksum: 622d6ebfa87551ddad978a95d5a84bc8 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / A endometriose é uma doença crônica multifatorial, inflamatória, estrógeno-dependente, que afeta entre 8 a 10% das mulheres em idade reprodutiva e caracterizada por tecido similar ao endométrio (glândula e estroma) fora da cavidade uterina. Embora a sua etiologia seja pouco conhecida, evidências recentes indicam que alterações epigenéticas estão envolvidas na sua patofisiologia. Esta hipótese é apoiada pelos achados envolvendo padrões alterados de metilação do DNA em genes específicos, bem como pelos níveis alterados de expressão de componentes da maquinaria epigenética nas lesões endometrióticas, quando comparadas ao endométrio eutópico da mesma paciente ou ao endométrio de mulheres que não apresentam a doença. Assim, um melhor entendimento do papel dos mecanismos epigenéticos na patogênese e progressão da endometriose tem se tornado necessário, podendo contribuir para a identificação de marcadores diagnósticos e para o delineamento de novas abordagens terapêuticas, que trariam benefícios e melhor qualidade de vida para as mulheres que apresentam esta condição. Neste contexto, este estudo buscou a identificação de genes diferencialmente metilados candidatos a biomarcadores na endometriose. Os resultados obtidos foram organizados em dois artigos científicos. O primeiro artigo teve como objetivo investigar o perfil diferencial de metilação do DNA na endometriose intestinal em comparação com amostras pareadas de endométrio eutópico da mesma paciente. Para isso, foi empregada uma abordagem em larga escala baseada em microarranjos contendo 27.800 ilhas CpG, que resultou na identificação de 546 genes hipermetilados e 871 genes hipometilados. A análise in silico para a classificação funcional dos genes diferencialmente metilados permitiu identificar conjuntos de genes com funções de fatores de transcrição, remodeladores da cromatina entre outras classes funcionais. Após a realização de uma ... / The endometriosis is a multi-factorial and chronic disease affecting 5% to 10% of women in reproductive age characterized by endometrium-like tissue (gland and stromma) outside uterine cavity. Although its etiology is poorly understood, recent evidences have indicated that epigenetic alterations are implicated in the pathophysiology. This hypothesis has been supported by findings surrounding altered DNA methylation pattern of specific genes, as well as by altered levels of expression of epigenetic machinery components in endometriotic lesions compared to eutopic endometrium from the same patient or endometrium of women free of disease. Thus, a better understanding of the role of epigenetic mechanisms in the pathogenesis and progression of endometriosis has become necessary and may contribute to the identification of diagnostic markers and for designing new therapeutic approaches that could benefit and improve the quality of life of women with this condition. In this context, this study aimed to identify differentially methylated genes as candidate biomarkers in endometriosis. The results could be organized in two papers. The first study aimed to investigate the profile of differential DNA methylation in intestinal endometriosis compared to eutopic endometrium of paired samples from the same patient. For this, we carried out a large-scale approach based on microarray containing 27,800 CpG islands, resulting in the identification of 546 genes as hypermethylated and 871 genes as hipomethylated. In silico analysis for the functional classification of differentially methylated genes enabled us to identify sets of genes with functions of transcription factors, chromatin remodeling, besides other functional classes. After conducting a comparative assessment with data available in other large-scale studies of literature, it was possible to recognize recurrent alteratons evolving 227 hypermethylated and 322 hypomethylated ...

Orientador: Cláudia Apaecida Rainho / Banca: Wellerson Rodrigo Scarano / Banca: Erika Cristina Pavarino / Banca: Adriana Camargo Ferrasi / Banca: Sandro José Conde / Resumo: A endometriose é uma doença crônica multifatorial, inflamatória, estrógeno-dependente, que afeta entre 8 a 10% das mulheres em idade reprodutiva e caracterizada por tecido similar ao endométrio (glândula e estroma) fora da cavidade uterina. Embora a sua etiologia seja pouco conhecida, evidências recentes indicam que alterações epigenéticas estão envolvidas na sua patofisiologia. Esta hipótese é apoiada pelos achados envolvendo padrões alterados de metilação do DNA em genes específicos, bem como pelos níveis alterados de expressão de componentes da maquinaria epigenética nas lesões endometrióticas, quando comparadas ao endométrio eutópico da mesma paciente ou ao endométrio de mulheres que não apresentam a doença. Assim, um melhor entendimento do papel dos mecanismos epigenéticos na patogênese e progressão da endometriose tem se tornado necessário, podendo contribuir para a identificação de marcadores diagnósticos e para o delineamento de novas abordagens terapêuticas, que trariam benefícios e melhor qualidade de vida para as mulheres que apresentam esta condição. Neste contexto, este estudo buscou a identificação de genes diferencialmente metilados candidatos a biomarcadores na endometriose. Os resultados obtidos foram organizados em dois artigos científicos. O primeiro artigo teve como objetivo investigar o perfil diferencial de metilação do DNA na endometriose intestinal em comparação com amostras pareadas de endométrio eutópico da mesma paciente. Para isso, foi empregada uma abordagem em larga escala baseada em microarranjos contendo 27.800 ilhas CpG, que resultou na identificação de 546 genes hipermetilados e 871 genes hipometilados. A análise in silico para a classificação funcional dos genes diferencialmente metilados permitiu identificar conjuntos de genes com funções de fatores de transcrição, remodeladores da cromatina entre outras classes funcionais. Após a realização de uma ... / Abstract: The endometriosis is a multi-factorial and chronic disease affecting 5% to 10% of women in reproductive age characterized by endometrium-like tissue (gland and stromma) outside uterine cavity. Although its etiology is poorly understood, recent evidences have indicated that epigenetic alterations are implicated in the pathophysiology. This hypothesis has been supported by findings surrounding altered DNA methylation pattern of specific genes, as well as by altered levels of expression of epigenetic machinery components in endometriotic lesions compared to eutopic endometrium from the same patient or endometrium of women free of disease. Thus, a better understanding of the role of epigenetic mechanisms in the pathogenesis and progression of endometriosis has become necessary and may contribute to the identification of diagnostic markers and for designing new therapeutic approaches that could benefit and improve the quality of life of women with this condition. In this context, this study aimed to identify differentially methylated genes as candidate biomarkers in endometriosis. The results could be organized in two papers. The first study aimed to investigate the profile of differential DNA methylation in intestinal endometriosis compared to eutopic endometrium of paired samples from the same patient. For this, we carried out a large-scale approach based on microarray containing 27,800 CpG islands, resulting in the identification of 546 genes as hypermethylated and 871 genes as hipomethylated. In silico analysis for the functional classification of differentially methylated genes enabled us to identify sets of genes with functions of transcription factors, chromatin remodeling, besides other functional classes. After conducting a comparative assessment with data available in other large-scale studies of literature, it was possible to recognize recurrent alteratons evolving 227 hypermethylated and 322 hypomethylated ... / Doutor

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Tecnologia, Departamento de Engenharia Elétrica, 2014. / Submitted by Ana Cristina Barbosa da Silva (annabds@hotmail.com) on 2014-11-25T17:23:31Z No. of bitstreams: 1 2014_RafaelCortesdePaiva.pdf: 7660330 bytes, checksum: eaad53db8e1c76edec638a3e30ee5f3e (MD5) / Approved for entry into archive by Raquel Viana(raquelviana@bce.unb.br) on 2014-11-25T17:58:53Z (GMT) No. of bitstreams: 1 2014_RafaelCortesdePaiva.pdf: 7660330 bytes, checksum: eaad53db8e1c76edec638a3e30ee5f3e (MD5) / Made available in DSpace on 2014-11-25T17:58:54Z (GMT). No. of bitstreams: 1 2014_RafaelCortesdePaiva.pdf: 7660330 bytes, checksum: eaad53db8e1c76edec638a3e30ee5f3e (MD5) / Nesse trabalho foi realizado o estudo de técnicas bio-inspiradas para gerar a marcha de um robô bípede. Foi utilizado o conceito de CPG, Central Pattern Generator (CPG), que é uma rede neural capaz de produzir respostas rítmicas. Elas foram modeladas como osciladores acoplados chamados de osciladores neurais. Para tanto foram utilizados alguns modelos de osciladores, o modelo de Matsuoka, o modelo de Kuramoto e o modelo de Kuramoto com acoplamento entre a dinâmica do oscilador e a dinâmica da marcha. Foram usados dois modelos de robôs, o Bioloid e o NAO. Para otimizar os parâmetros dos osciladores foram utilizados o Algoritmo Genético (AG), o Particle Swarm Optimization (PSO) e o Nondominated sorting Genetic Algorithm II (NSGA-II). Foi utilizada uma função de custo que através de determinadas condições tem como objetivo obter uma marcha eficiente. No NSGA-II, além dessa função de custo, foi utilizada outra função de custo que considera o trabalho realizado pelo robô. Além disso, também foi utilizada a aprendizagem por reforço para treinar um controlador que corrige a postura do robô durante a marcha. Foi possível propor um framework para obter os parâmetros dos osciladores e através dele obter uma marcha estável em ambas as plataformas. Também foi possível propor um framework utilizando aprendizagem por reforço para treinar um controlador para corrigir a postura do robô com a marcha sendo gerado pelo oscilador de Kuramoto com acoplamento. O objetivo do algoritmo foi minimizar a velocidade do ângulo de arfagem do corpo do robô, dessa forma, a variação do ângulo de arfagem também foi minimizada consequentemente. Além disso, o robô andou mais “cautelosamente” para poder manter a postura e dessa forma percorreu uma distância menor do que se estivesse sem o controlador. ______________________________________________________________________________ ABSTRACT / This document describes computational optimized bipedal robot gait generators. Thegaits are applied by a neural oscillator, composed of coupled central pattern generators(CPG), which are neural networks capable of producing rhythmic output. The models ofthe oscillators used were the Matsuoka model, Kuramoto model and Kura moto model withcoupling between the dynamics of the oscillator and dynamics of the gait. Two bipedalrobots, a NAO and a Bioloid, were used. The neural oscillators were optimized with threealgorithms, a Genetic Algorithm (GA), Particle Swarm Optimization (PSO) and Nondominatedsorting Genetic Algorithm II (NSGA-II). It was used a fitness function that has theobjective to obtain an efficient gait through some conditions. In NSGA-II, besides this fitnessfunction, another one was used that has the objective to minimize the work done by therobot. Additionally, reinforcement learning techniques were used to train a controller thatcorrects the robots gait posture. It was proposed a framework to obtain the parameters of theoscillators used and obtain efficient gaits in both robots. Also, it was proposed a frameworkusing reinforcement learning to train a controller to correct the robots gait posture. The objective of the algorithm was to minimize the pitch angular velocity, consequently the pitchangle standard deviation was minimized. Additionally, the robot moved with more “caution” and walked less compared with the walk without the posture controller.

Made available in DSpace on 2014-06-12T15:56:32Z (GMT). No. of bitstreams: 2 arquivo2952_1.pdf: 2916037 bytes, checksum: 4c0ccce80d7e4bc503fb235119194f20 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2010 / Faculdade de Amparo à Ciência e Tecnologia do Estado de Pernambuco / Este trabalho esta situado na área de controle e gerenciamento de locomoção de robôs com membros e apresenta um novo modelo de rede neural, o STRAGIC (Gerador de Trajetórias de Estados com Inter-Conexões), bem como outros modelos de redes neurais aplicadas a este domínio do conhecimento. O STRAGIC foi projetado a partir do STRAGEN, um mapa auto-organizável de topologia variável. O STRAGIC controla a locomoção do robô por meio de uma trajetória de estados que descreve a postura do robô em intervalos regulares de tempo. Alguns ambientes de teste foram elaborados para verificar a capacidade do STRAGIC em: controlar o robô com um determinado modo de locomoção; controlar o robô a partir de dados ruidosos; controlar o robô a partir de uma base de dados com estados de diferentes trajetórias; gerenciar a transição entre modos de locomoção; e por fim extrair trajetórias de estados a partir da locomoção de um animal real. Além disso, faz um estudo de dois parâmetros importantes do STRAGEN

Dans cette thèse, on a travaillé sur 3 plantes médicinales : Ammoides pusilla, Pituranthos tortuosus et Tetraclinis articulata. L'objectif était : (i) d'identifier la composition chimique des extraits organiques et des huiles essentielles issues de ces plantes, (ii) établir un screening biologiques in vitro des activité anti-Alzheimer, anti-Superoxyde dismutase, anti-xanthine oxidase, antidiabétique, anti-inflammatoire et anti-cancer (iii) évaluer in vivo le pouvoir hépatoprotecteur et anti-inflammatoire de A. pusilla, (iv) étudier l'activité litholytique de l'extrait aqueux d'A. pusilla contre différents types de calculs rénaux et (v) déterminer la relation structure-activités de 20 flavonoïdes. Les extraits organiques ont été obtenus par extraction avec des solvants de polarité croissante. D'autre part, une hydrodistillation a permis d'extraire les huiles essentielles de chaque partie aérienne. Une caractérisation de la composition chimique de ces extraits/huiles essentielles a été établie par CPG-SM/CG-FID et HPLC (pour les extraits). L'activité anti-cancer a été réalisée par le test MTT sur des lignées cellulaires différentes. Pour A. pusilla, 2 nouveaux composés ont été identifiés dans l'extrait de cyclohexane et 4 nouveaux composés dans l'extrait de dichlorométhane. L'effet hépato protecteur de l'extrait d'A. pusilla sur le foie a été mis en évidence. L'extrait de dichlorométhane a permis d'obtenir 77,02% d'inhibition, pour l'activité anti-inflammatoire in vivo. Pour P. tortuosus, 17 composés ont été détectés dans l'huile essentielle pour la première fois. Pour les 20 flavonoïdes testés le pouvoir antioxydant a été corrélé à des propriétés biologiques. Cinq types de calculs rénaux différents ont été identifiés (typologie et composition élémentaire) par MEB/EDX. A. pusilla a présenté une activité litholytique à 100% pour les calculs rénaux de type urinaire et oxalate de calcium. / In this thesis, we worked on 3 medicinal plants: Ammoides pusilla, Pituranthos tortuosus and Tetraclinis articulata. The aim was: (i) identify the chemical composition of organic extracts and essential oils from these plants, (ii) establish a biological screening of in vitro anti-Alzheimer, anti-superoxide dismutase, anti-xanthine oxidase , anti-diabetic, anti-inflammatory and anti-cancer activities (iii) evaluate in vivo hepatoprotective and anti-inflammatory power of A. pusilla, (iv) study litholytic activity of aqueous extract of A. pusilla against different types of kidney stones and (v) determine the relationship structure-activity of 20 flavonoids. The organic extracts were obtained by extraction with solvents of increasing polarity. Furthermore, a hydrodistillation was used to extract essential oils from each aerial part. A characterization of the chemical composition of these extracts / essential oils was determined by GC-MS/GC-FID and HPLC (for extracts). The anti-cancer activity was carried out by MTT assay on different cell lines. For A. pusilla, two novel compounds were identified in the extract of cyclohexane and 4 novel compounds in the dichloromethane extract. A. pusilla hepatoprotective effect on the liver has been highlighted. The dichloromethane extract of P. tortuosus gives 77.02% inhibition for in vivo anti-inflammatory activity, 17 compounds were detected in the essential oil for the first time. For the 20 flavonoids tested the antioxidant power was correlated with biological properties. Five different types of kidney stones have been identified (typology and elemental composition) using SEM / EDX. A. pusilla litholytic activity presented at 100% for urinary-type and calcium oxalate kidney stones.

No description available.

Background. Toll-like receptors (TLRs) play a role in the pathophysiology of sepsis and multiple organ failure. This study examined the effect of CpG oligodeoxynucleotide (CpG-ODN), the TLR9 ligand, on polymicrobial sepsis-induced cardiac dysfunction.Methods. Male C57BL/6 mice were treated with CpG-ODN, control CpG-ODN (control-ODN), or inhibitory CpG-ODN (iCpG-ODN) 1 hour prior to cecal ligation and puncture (CLP)-induced sepsis. Mice that underwent sham surgery served as sham controls. Cardiac function was examined by echocardiography before and 6 hours after CLP.Results. Cardiac function was significantly decreased 6 hours after CLP. CpG-ODN prevented CLP-induced cardiac dysfunction, as evidenced by maintenance of the ejection fraction and fractional shortening. Control-ODN or iCpG-ODN did not alter CLP-induced cardiac dysfunction. CpG-ODN significantly attenuated CLP-induced myocardial apoptosis and increased myocardial Akt and extracellular-signal-related kinase (ERK) phosphorylation levels following CLP. In vitro experiments demonstrated that CpG-ODN promotes an association between TLR9 and Ras, resulting in Akt and ERK phosphorylation. Inhibition of phosphoinositide 3-kinase (PI3K) by Ly294002 or inhibition of ERK by U0126 in vivo abolished CpG-ODN attenuation of CLP-induced cardiac dysfunction.Conclusions. CpG-ODN prevents CLP-induced cardiac dysfunction, in part through activation of PI3K/Akt and ERK signaling. Modulation of TLR9 could be an effective approach for treatment of cardiovascular dysfunction in patients with sepsis or septic shock.