Resumo: O gênero Zaprionus tem sido eleito como um bom modelo biológico para estudos genéticocomparativos com as espécies do subgrupo melanogaster do gênero Drosophila, embora seu posicionamento filogenético dentro da família Drosophilidae ainda seja controverso. Na presente Tese foi investigada a presença de 10 elementos de transposição (TEs) em Zaprionus indianus e Drosophila malerkotliana, bem como a distribuição, a atividade transcricional e as relações evolutivas de três retrotransposons (copia, gypsy e micropia) em sete espécies do gênero Zaprionus. Para isso, foram empregadas as técnicas de Dot blot, PCR, RT-PCR e seqüenciamento. As seqüências obtidas foram comparadas às dos respectivos elementos das demais espécies de drosofilídeos disponíveis nas bases de dados genômicas. Os resultados indicam que Z. indianus e D. malerkotliana apresentam em seus genomas todos os TEs de D. melanogaster investigados. O retrotransposon copia foi seqüenciado e está transcricionalmente ativo nas sete espécies do gênero Zaprionus e constitui uma nova subfamília relacionada aos elementos do subgrupo melanogaster, que foi denominada subfamília GBFDouble-gap. Por outro lado, os retrotransposons gypsy e micropia foram identificados nas espécies do subgênero Zaprionus, onde também estão transcricionalmente ativos, e pertencem às subfamílias já descritas para as espécies do subgrupo melanogaster. As análises evolutivas sugeriram que esses três retrotransposons devem ter participado de eventos de transferência horizontal com as espécies do subgrupo melanogaster e com pelo menos um doador desconhecido, no caso do retrotransposon micropia. Além disso, o cálculo dos tempos de divergência dos elementos sugere que eles passaram por ondas de transferências horizontais, mais antigas para o retrotransposon copia, e mais recentes para gypsy e micropia. Esses resultados... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The Zaprionus genus has been elected as a good biological model for comparative analyses with the melanogaster subgroup of Drosophila genus, though its phylogenetic positioning within the Drosophilidae family is still controversial. This study aiming at investigating the occurrence of 10 transposable elements (TEs) in Zaprionus indianus and Drosophila malerkotliana species, as well the distribution, transcriptional activity and evolutionary relationships of three retrotransposons (copy, gypsy and micropia) in seven species of Zaprionus genus. To do so, Dot blot, PCR, RT-PCR and sequencing methods were employed. The Zaprionus sequences obtained were compared with the drosophilid sequences available in genomic databases. The results indicated that Z. indianus and D. malerkotliana harbor all D. melanogaster TEs investigated. The copia retrotransposon is present and transcriptionally active in seven species of the Zaprionus genus and represents a new subfamily related to that of the melanogaster subgroup, named as GBFDouble-gap subfamily. Additionally, gypsy and micropia retrotransposons were identified in the Zaprionus species subgenus, which are transcriptionally active and belong to the melanogaster subgroup subfamilies. The evolutionary analysis showed the three retrotransposons could have been involved in horizontal transfer events with species of the melanogaster subgroup for the three retrotransposons and at least one unknown donor regarding to micropia retrotransposon. Moreover, the time of divergence seems to indicate that the retrotransposons experienced horizontal transfer waves, the oldest involving the copia element followed by the gypsy and micropia retrotransposons in more recent times. These results suggest that the horizontal transfer phenomenon has happened repeatedly during the Zaprionus genus and melanogaster subgroup evolution in the Afrotropical region. / Orientador: Cláudia Márcia Aparecida Carareto / Coorientador: Marie Anne Van Sluys / Banca: Hermione Elly Melara de Campos Bicudo / Banca: Maria Magdalena Rossi / Banca: Galina Ananina / Banca: Elgion da Silva Loreto / Doutor

We present an efficient quantum algorithm for the Hidden Subgroup Problem (HSP) on the semidirect product of the cyclic groups and , where is any odd prime number, and are positives integers and the homomorphism which defines the group is given by the root such that . As a consequence we can solve efficiently de HSP on the semidirect product of the groups by , where has a special prime factorization. / Neste trabalho apresentamos um algoritmo quântico eficiente para o Problema do Subgrupos Oculto (PSO) no produto semidireto dos grupos cíclicos e , onde é qualquer número primo ímpar, e são inteiros positivos e o homomorfismo que define o grupo é dado por uma raiz para a qual . Como conseqüência, podemos resolver eficientemente o PSO também no produto semidireto dos grupos por , onde o inteiro possui uma especial fatoração prima.

Neste trabalho apresentamos um novo algoritmo quântico eficiente para o Problema do Subgrupo Oculto (PSO) sobre uma classe especial de grupos metacíclicos, Z_p times Z_q^s, com q | (p-1) e p/q= poli(log p), onde p, q são números primos ímpares distintos e s um inteiro positivo qualquer. Em um contexto mais geral, sem impor uma relação entre p e q obtemos um algoritmo quântico com complexidade de tempo 2^{O(sqrt{log p})}. Em qualquer caso, esses resultados são melhores que qualquer algoritmo clássico para o mesmo fim, cuja complexidade é Omega(sqrt{p}). Apresentamos também, algoritmos quânticos para o PSO sobre grupos não abelianos de ordem 2^{n+1} que possuem subgrupos cíclicos de índice 2 e para certos produtos semidiretos de grupos Z_N^m times Z_p, com m, N inteiros positivos e N fatorado de forma especial. / We present a new polynomial-time quantum algorithm that solves the hidden subgroup problem (HSP) for a special class of metacyclic groups, namely Z_{p} times _{q^s}, with q mid (p-1) and p/q= up{poly}(log p), where p, q are any odd prime numbers and s is any positive integer. This solution generalizes previous algorithms presented in the literature. In a more general setting, without imposing a relation between p and q, we obtain a quantum algorithm with time and query complexity 2^{O(sqrt{log p})}. In any case, those results improve the classical algorithm, which needs {Omega}(sqrt{p}) queries. We also present quantum algorithms for the HSP over non-abelian groups of order 2^{n+1} which have a cyclic subgroup of index 2 and for some semidirect product _N^m times _p, where N has a special prime factorization.

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The intermontane Ipswich Basin, which is situated 30km south-west of Brisbane, contains coal measures formed in the Late Triassic Epoch following a barren non-depositional period. Coal, tuff, and basalt were deposited along with fluvial dominated sediments. The Ipswich Coal Measures mark the resumption of deposition in eastern Australia after the coal hiatus associated with a series of intense tectonic activity in Gondwanaland during the Permo-Triassic interval. A transtensional tectonic movement at the end of the Middle Triassic deformed the Toogalawah Group before extension led to the formation of the Carnian Ipswich Coal Measures in the east. The Ipswich Coal Measures comprise the Brassall and Kholo Subgroups. The Blackstone Formation, which forms the upper unit of the Brassall Subgroup, contains seven major coal seams. The lower unit of the Brassall Subgroup, the Tivoli Formation, consists of sixteen stratigraphically significant coal seams. The typical thickness of the Blackstone Formation is 240m and the Tivoli Formation is about 500m. The coal seams of the Ipswich Basin differ considerably from those of other continental Triassic basins. However, the coal geology has previously attracted little academic attention and the remaining exposures of the Ipswich coalfield are rapidly disappearing now that mining has ceased. The primary aim of this project was to study the patterns of coal sedimentation and the response of coal seam characteristics to changing depositional environments. The coal accumulated as a peat-mire in an alluvial plain with meandering channel systems. Two types of peat-mire expansion occurred in the basin. Peat-mire aggradation, which is a replacement of water body by the peatmire, was initiated by tectonic subsidence. This type of peat-mire expansion is known as terrestrialisation. It formed thick but laterally limited coal seams in the basin. Whereas, peat-mire progradation was related to paludification and produced widespread coal accumulation in the basin. The coal seams were separated into three main groups based on the mean seam thickness and aerial distribution of one-meter and four-meter thickness contour intervals. Group 1 seams within the one-meter thickness interval are up to 15,000m2 in area, and seams within the four-meter interval have an aerial extent of up to 10,000m2. Group 1A contains the oldest seam with numerous intraseam clastic bands and shows a very high thickness to area ratio, which indicates high subsidence rates. Group 1B seams have moderately high thickness to area ratios. The lower clastic influx and slower subsidence rates favoured peat-mire aggradation. The Group 1A seam is relatively more widespread in aerial extent than seams from Group 1B. Group 1C seams have low mean thicknesses and small areas, suggesting short-lived peat-mires as a result of high clastic influx. Group 2 seams arebetween 15,000 and 35,000m2 in area within the one-meter interval, and between 5,000 and 10,000m2 within the four-meter interval. They have moderately high area to thickness ratios, indicating that peat-mire expansion occurred due to progressively shallower accommodation and a rising groundwater table. Group 3 seams, which have aerial extents from 35,000 to 45,000m2 within the one-meter thickness contour interval and from 10,000 to 25,000m2 within the four-meter interval, show high aerial extent to thickness ratios. They were deposited in quiet depositional environments that favoured prolonged existence of peat-mires. Group 3 seams are all relatively young whereas most Group 1 seams are relatively old seams. All the major fault systems, F1, F2 and F3, trend northwest-southeast. Apart from the West Ipswich Fault (F3), the F1 and F2 systems are broad Palaeozoic basement structures and thus they may not have had a direct influence on the formation of the much younger coal measures. However, the sedimentation patterns appear to relate to these major fault systems. Depocentres of earlier seams in the Tivoli Formation were restricted to the northern part of the basin, marked by the F1 system. A major depocentre shift occurred before the end of the deposition of the Tivoli Formation as a result of subsidence in the south that conformed to the F2 system configuration. The Blackstone Formation depocentres shifted to the east (Depocentre 1) and west (Depocentre 2) simultaneously. This depocentre shift was associated with the flexural subsidence produced by the rejuvenation of the West Ipswich Fault. Coal accumulation mainly occurred in Depocentre 1. Two types of seam splitting occurred in the Ipswich Basin. Sedimentary splitting or autosedimentation was produced by frequent influx of clastic sediments. The fluvial dominant depositional environments created the random distribution of small seam splits. However, the coincidence of seam splits and depocentres found in some of the seams suggests tectonic splitting. Furthermore, the progressive splitting pattern, which displays seam splits overlapping, was associated with continued basin subsidence. The tectonic splitting pattern is more dominant in the Ipswich Basin. Alternating bright bands shown in the brightness profiles are a result of oscillating water cover in the peat-mire. Moderate groundwater level, which was maintained during the development of the peat, reduced the possibility of salinisation and drowning of the peat swamp. On the other hand, a slow continuous rise of the groundwater table, that kept pace with the vertical growth of peat, prevented excessive oxidation of peat. Ipswich coal is bright due to its high vitrinite content. The cutinite content is also high because the dominant flora was pteridosperms of Dicroidium assemblage containing waxy and thick cuticles. Petrographic study revealed that the depositional environment was telmatic with bog forest formed under ombrotrophic to mesotrophic hydrological conditions. The high preservation of woody or structured macerals such as telovitrinite and semifusinite indicates that coal is autochthonous. The high mineral matter content in coal is possibly due to the frequent influx of clastic and volcanic sediments. The Ipswich Basin is part of a much larger Triassic basin extending to Nymboida in New South Wales. Little is known of the coal as it lacks exposures. It is apparently thin to absent except in places like Ipswich and Nymboida. This study suggests that the dominant control on depocentres of thick coal at Ipswich has been the tectonism. Fluvial incursions and volcanism were superimposed on this.

Protein sequencing has produced overwhelming amount of protein sequences, especially in the last decade. Nevertheless, the majority of the proteins' functional and structural classes are still unknown, and experimental methods currently used to determine these properties are very expensive, laborious and time consuming. Therefore, automated computational methods are urgently required to accurately and reliably predict functional and structural classes of the proteins. Several bioinformatics methods have been developed to determine such properties of the proteins directly from their sequence information. Such methods that involve signal processing methods have recently become popular in the bioinformatics area and been investigated for the analysis of DNA and protein sequences and shown to be useful and generally help better characterise the sequences. However, there are various technical issues that need to be addressed in order to overcome problems associated with the signal processing methods for the analysis of the proteins sequences. Amino acid indices that are used to transform the protein sequences into signals have various applications and can represent diverse features of the protein sequences and amino acids. As the majority of indices have similar features, this project proposes a new set of computationally derived indices that better represent the original group of indices. A study is also carried out that resulted in finding a unique and universal set of best discriminating amino acid indices for the characterisation of allergenic proteins. This analysis extracts features directly from the protein sequences by using Discrete Fourier Transform (DFT) to build a classification model based on Support Vector Machines (SVM) for the allergenic proteins. The proposed predictive model yields a higher and more reliable accuracy than those of the existing methods. A new method is proposed for performing a multiple sequence alignment. For this method, DFT-based method is used to construct a new distance matrix in combination with multiple amino acid indices that were used to encode protein sequences into numerical sequences. Additionally, a new type of substitution matrix is proposed where the physicochemical similarities between any given amino acids is calculated. These similarities were calculated based on the 25 amino acids indices selected, where each one represents a unique biological protein feature. The proposed multiple sequence alignment method yields a better and more reliable alignment than the existing methods. In order to evaluate complex information that is generated as a result of DFT, Complex Informational Spectrum Analysis (CISA) is developed and presented. As the results show, when protein classes present similarities or differences according to the Common Frequency Peak (CFP) in specific amino acid indices, then it is probable that these classes are related to the protein feature that the specific amino acid represents. By using only the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient, as biologically related features can appear individually either in the real or the imaginary spectrum. This is successfully demonstrated over the analysis of influenza neuraminidase protein sequences. Upon identification of a new protein, it is important to single out amino acid responsible for the structural and functional classification of the protein, as well as the amino acids contributing to the protein's specific biological characterisation. In this work, a novel approach is presented to identify and quantify the relationship between individual amino acids and the protein. This is successfully demonstrated over the analysis of influenza neuraminidase protein sequences. Characterisation and identification problem of the Influenza A virus protein sequences is tackled through a Subgroup Discovery (SD) algorithm, which can provide ancillary knowledge to the experts. The main objective of the case study was to derive interpretable knowledge for the influenza A virus problem and to consequently better describe the relationships between subtypes of this virus. Finally, by using DFT-based sequence-driven features a Support Vector Machine (SVM)-based classification model was built and tested, that yields higher predictive accuracy than that of SD. The methods developed and presented in this study yield promising results and can be easily applied to proteomic fields.

Cette thèse s'intéresse à la cohomologie de fibrés en droite sur le fibré cotangent de variétés projectives. Plus précisément, pour $G$ un groupe algébrique simple, connexe et simplement connexe, $P$ un sous-groupe maximal de $G$ et $\omega$ un générateur dominant du groupe de caractères de $P$, on cherche à comprendre les groupes de cohomologie $H^i(T^*(G/P),\mathcal{L})$ où $\mathcal{L}$ est le faisceau des sections d'un fibré en droite sur $T^*(G/P)$. Sous certaines conditions, nous allons montrer qu'il existe un isomorphisme, à graduation près, entre $H^i(T^*(G/P),\mathcal{L})$ et $H^i(T^*(G/P),\mathcal{L}^{\vee})$ Après avoir travaillé dans un contexte théorique, nous nous intéresserons à certains sous-groupes paraboliques en lien avec les orbites nilpotentes. Dans ce cas, l'algèbre de Lie du radical unipotent de $P$, que nous noterons $\nLie$, a une structure d'espace vectoriel préhomogène. Nous pourrons alors déterminer quels cas vérifient les hypothèses nécessaires à la preuve de l'isomorphisme en montrant l'existence d'un $P$-covariant $f$ dans $\comp[\nLie]$ et en étudiant ses propriétés. Nous nous intéresserons ensuite aux singularités de la variété affine $V(f)$. Nous serons en mesure de montrer que sa normalisation est à singularités rationnelles. / In this thesis, we study the cohomology of line bundles on cotangent bundle of projective varieties. To be more precise, let $G$ be an semisimple algebraic group which is simply connected, $P$ a maximal subgroup and $\omega$ a dominant weight that generates the character group of $P$. Our goal is to understand the cohomology groups $H^i(T^*(G/P),\mathcal{L})$ where $\mathcal{L}$ is the sheaf of sections of a line bundle on $T^*(G/P)$. Under some conditions, we will show that there exists an isomorphism, up to grading, between $H^i(T^*(G/P),\mathcal{L})$ and $H^i(T^*(G/P),\mathcal{L}^{\vee})$. After we worked in a theoretical setting, we will focus on maximal parabolic subgroups related to nilpotent varieties. In this case, the Lie algebra of the unipotent radical of $P$ has a structure of prehomogeneous vector spaces. We will be able to determine which cases verify the hypothesis of the isomorphism by showing the existence of a $P$-covariant $f$ in $\comp[\nLie]$ and by studying its properties. We will be interested by the singularities of the affine variety $V(f)$. We will show that the normalisation of $V(f)$ has rational singularities.

Dans cette thèse, nous nous intéressons à des compactifications géométriques variées. Nous décrivons l'espace des sous-groupes fermés du groupe RxZ. Nous étudions la compactification de Chabauty des espaces symétriques de type non compact. Nous définissons et étudions la compactification de Chabauty de l'espace des plats maximaux des espaces symétriques de SL3(R) et de SL4(R). Nous étudions les limites géométriques de plats maximaux de l'espace symétrique ou de l'immeuble de Bruhat-Tits associé à SL3 sur un corps local. Nous définissons et étudions une compactification à la Thurston des espaces de classes d'isométrie de réseaux marqués. Nous définissons une compactification à la Thurston de l'espace de Torelli d'une surface et nous décrivons la stratification naturelle d'une partie de son bord. / In our thesis, we focus on various geometric compactifications. We describe the space of closed subgroups of RxZ. We study the Chabauty compactification of symmetric spaces of non-compact type. We define and study the Chabauty compactification of the space of maximal flats of the symmetric spaces of SL3(R) and SL4(R). We study the geometric limits of maximal flats in the symmetric space or in the Bruhat-Tits building associated to SL3 over a local field. We define and study a Thurston-like compactification of spaces of isometry classes of marked lattices. We define a Thurston-like compactification of the Torelli space of a surface and we describe the natural stratification of a subset of the boundary.

Made available in DSpace on 2015-03-04T18:50:57Z (GMT). No. of bitstreams: 1 Tese-Carlos-Magno1.pdf: 616333 bytes, checksum: 65e51c95902afd18d11a1d7366653fc0 (MD5) Previous issue date: 2008-03-13 / Conselho Nacional de Desenvolvimento Cientifico e Tecnologico / We present an efficient quantum algorithm for the Hidden Subgroup Problem (HSP) on the semidirect product of the cyclic groups and , where is any odd prime number, and are positives integers and the homomorphism which defines the group is given by the root such that . As a consequence we can solve efficiently de HSP on the semidirect product of the groups by , where has a special prime factorization. / Neste trabalho apresentamos um algoritmo quântico eficiente para o Problema do Subgrupos Oculto (PSO) no produto semidireto dos grupos cíclicos e , onde é qualquer número primo ímpar, e são inteiros positivos e o homomorfismo que define o grupo é dado por uma raiz para a qual . Como conseqüência, podemos resolver eficientemente o PSO também no produto semidireto dos grupos por , onde o inteiro possui uma especial fatoração prima.

Made available in DSpace on 2015-03-04T18:51:16Z (GMT). No. of bitstreams: 1 Tese Demerson.pdf: 742439 bytes, checksum: 534128a7d9b5cfc57f84985cd77ac16d (MD5) Previous issue date: 2009-08-28 / We present a new polynomial-time quantum algorithm that solves the hidden subgroup problem (HSP) for a special class of metacyclic groups, namely Z_{p} \rtimes \Z_{q^s}, with q \mid (p-1) and p/q= \up{poly}(\log p), where p, q are any odd prime numbers and s is any positive integer. This solution generalizes previous algorithms presented in the literature. In a more general setting, without imposing a relation between p and q, we obtain a quantum algorithm with time and query complexity 2^{O(\sqrt{\log p})}. In any case, those results improve the classical algorithm, which needs {\Omega}(\sqrt{p}) queries. We also present quantum algorithms for the HSP over non-abelian groups of order 2^{n+1} which have a cyclic subgroup of index 2 and for some semidirect product \Z_N^m \rtimes \Z_p, where N has a special prime factorization. / Neste trabalho apresentamos um novo algoritmo quântico eficiente para o Problema do Subgrupo Oculto (PSO) sobre uma classe especial de grupos metacíclicos, Z_p \rtimes Z_q^s, com q | (p-1) e p/q= poli(log p), onde p, q são números primos ímpares distintos e s um inteiro positivo qualquer. Em um contexto mais geral, sem impor uma relação entre p e q obtemos um algoritmo quântico com complexidade de tempo 2^{O(\sqrt{log p})}. Em qualquer caso, esses resultados são melhores que qualquer algoritmo clássico para o mesmo fim, cuja complexidade é \Omega(\sqrt{p}). Apresentamos também, algoritmos quânticos para o PSO sobre grupos não abelianos de ordem 2^{n+1} que possuem subgrupos cíclicos de índice 2 e para certos produtos semidiretos de grupos Z_N^m \rtimes Z_p, com m, N inteiros positivos e N fatorado de forma especial.