Mycoplasma hyopneumoniae é uma bactéria de tamanho diminuto, caracterizada por um genoma pequeno, com baixo conteúdo GC. Está associada com doenças respiratórias de suínos, resultando em prejuízos produtivos e econômicos na indústria animal. A presença de sequências de DNA repetitivas, que ocorrem em grandes quantidades em células eucarióticas, vem sendo cada vez mais identificadas em genomas de procariotos, sendo também associadas a um potencial papel regulador. Uma vez que a regulação da transcrição nesses organismos ainda é pouco entendida, o objetivo do presente estudo foi realizar uma busca in silico por elementos repetitivos nas regiões intergênicas do genoma de M. hyopneumoniae linhagem 7448. Dois tipos de repetições foram selecionados para a busca inicial: tandem e palindromes. Regiões intergênicas de até 500 pb a montante do sítio de início da tradução de todas as CDSs do genoma de M. hyopneumoniae linhagem 7448 foram utilizadas para a predição. Para cada tipo de elemento dois programas computacionais independentes foram utilizados. As predições in silico resultaram em 144 repetições em tandem e 1.171 palindromes. O DNA repetitivo se encontra distribuído a montante de 86% das unidades transcricionais de M. hyopneumoniae linhagem 7448. Análises comparativas entre genomas de micoplasmas demonstraram diferentes níveis de conservação dos elementos repetitivos entre linhagens patogênicas e não-patogênicas. Linhagens patogênicas revelaram uma conservação de 59%, enquanto que a não patogênica, somente de 46%. Através de ensaios de amplificação quantitativa de DNA, foi observado diferentes níveis de expressão em genes codificantes para importantes proteínas, como glicina hidroximetiltransferase, lipoproteína, adesinas e proteína ligadora de GTP. Os genes codificantes para essas proteínas divergiam no número de repetições palindromes e tandens na sua respectiva região intergênica. Além disso, repetições encontradas em 206 genes já descritos como regulados em diferentes condições em M. hyopneumoniae linhagem 232 mostraram aproximadamente 80% de conservação em relação à linhagem M. hyopneumoniae linhagem 7448. Todos esses resultados sugerem um potencial papel regulador das repetições de DNA em tandem e palindromes em Mycoplasma. / Mycoplasma hyopneumoniae is a diminutive bacterium, characterized by a small genome with a low GC content. It is commonly associated with swine respiratory diseases, resulting in productivity and economic losses in the animal industry. Repetitive DNA, which occurs in large quantities in eukaryotic cells, has been increasingly identified in prokaryotic genomes, and has been associated with a potential regulatory function. Once transcription regulation in these organisms is still poorly understood, the aim of the current study was to perform an in silico search of repeat elements in the genomic intergenic regions of M. hyopneumoniae strain 7448. Two types of repeats were selected for initial search: Tandem and Palindromic. Intergenic regions up to 500 bp upstream from start codon of M. hyopneumoniae strain 7448 CDSs were used as input for the software’s prediction. For each type of repeat sequence, two independent software packages were used. Computational analysis results in 144 tandem repeats and 1,171 palindrome elements. The repeats were distributed in the upstream region of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct mycoplasmas, demonstrate different indices of repeat conservation among pathogenic and non-pathogenic strains. Pathogenic strains revealed 59% conservation, while non-pathogenic only 46%. Through assays of quantitative amplification of DNA, different levels of expression in genes coding important proteins have been demonstrated, as glycine hydroxymethyltransferase, lipoprotein, adhesins and GTP-binding protein. These protein coding genes differ in number of palindromes or tandem repeats in respective upstream regions. In addition, repeats found in 206 genes already described to be regulated in different grow conditions in M. hyopneumoniae strain 232 showed almost 80% of conservation in relation to M. hyopneumoniae strain 7448. All these findings, suggests a potential regulatory role of tandem and palindrome DNA repeats.

Mycoplasma hyopneumoniae é uma bactéria de tamanho diminuto, caracterizada por um genoma pequeno, com baixo conteúdo GC. Está associada com doenças respiratórias de suínos, resultando em prejuízos produtivos e econômicos na indústria animal. A presença de sequências de DNA repetitivas, que ocorrem em grandes quantidades em células eucarióticas, vem sendo cada vez mais identificadas em genomas de procariotos, sendo também associadas a um potencial papel regulador. Uma vez que a regulação da transcrição nesses organismos ainda é pouco entendida, o objetivo do presente estudo foi realizar uma busca in silico por elementos repetitivos nas regiões intergênicas do genoma de M. hyopneumoniae linhagem 7448. Dois tipos de repetições foram selecionados para a busca inicial: tandem e palindromes. Regiões intergênicas de até 500 pb a montante do sítio de início da tradução de todas as CDSs do genoma de M. hyopneumoniae linhagem 7448 foram utilizadas para a predição. Para cada tipo de elemento dois programas computacionais independentes foram utilizados. As predições in silico resultaram em 144 repetições em tandem e 1.171 palindromes. O DNA repetitivo se encontra distribuído a montante de 86% das unidades transcricionais de M. hyopneumoniae linhagem 7448. Análises comparativas entre genomas de micoplasmas demonstraram diferentes níveis de conservação dos elementos repetitivos entre linhagens patogênicas e não-patogênicas. Linhagens patogênicas revelaram uma conservação de 59%, enquanto que a não patogênica, somente de 46%. Através de ensaios de amplificação quantitativa de DNA, foi observado diferentes níveis de expressão em genes codificantes para importantes proteínas, como glicina hidroximetiltransferase, lipoproteína, adesinas e proteína ligadora de GTP. Os genes codificantes para essas proteínas divergiam no número de repetições palindromes e tandens na sua respectiva região intergênica. Além disso, repetições encontradas em 206 genes já descritos como regulados em diferentes condições em M. hyopneumoniae linhagem 232 mostraram aproximadamente 80% de conservação em relação à linhagem M. hyopneumoniae linhagem 7448. Todos esses resultados sugerem um potencial papel regulador das repetições de DNA em tandem e palindromes em Mycoplasma. / Mycoplasma hyopneumoniae is a diminutive bacterium, characterized by a small genome with a low GC content. It is commonly associated with swine respiratory diseases, resulting in productivity and economic losses in the animal industry. Repetitive DNA, which occurs in large quantities in eukaryotic cells, has been increasingly identified in prokaryotic genomes, and has been associated with a potential regulatory function. Once transcription regulation in these organisms is still poorly understood, the aim of the current study was to perform an in silico search of repeat elements in the genomic intergenic regions of M. hyopneumoniae strain 7448. Two types of repeats were selected for initial search: Tandem and Palindromic. Intergenic regions up to 500 bp upstream from start codon of M. hyopneumoniae strain 7448 CDSs were used as input for the software’s prediction. For each type of repeat sequence, two independent software packages were used. Computational analysis results in 144 tandem repeats and 1,171 palindrome elements. The repeats were distributed in the upstream region of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct mycoplasmas, demonstrate different indices of repeat conservation among pathogenic and non-pathogenic strains. Pathogenic strains revealed 59% conservation, while non-pathogenic only 46%. Through assays of quantitative amplification of DNA, different levels of expression in genes coding important proteins have been demonstrated, as glycine hydroxymethyltransferase, lipoprotein, adhesins and GTP-binding protein. These protein coding genes differ in number of palindromes or tandem repeats in respective upstream regions. In addition, repeats found in 206 genes already described to be regulated in different grow conditions in M. hyopneumoniae strain 232 showed almost 80% of conservation in relation to M. hyopneumoniae strain 7448. All these findings, suggests a potential regulatory role of tandem and palindrome DNA repeats.

Submitted by admin tede (tede@pucgoias.edu.br) on 2017-04-27T12:29:11Z No. of bitstreams: 1 RAFAEL SOUZA BONIFÁCIO.pdf: 1138929 bytes, checksum: 39a4b1bda2dfd94d3eea7bbd3c234fc3 (MD5) / Made available in DSpace on 2017-04-27T12:29:11Z (GMT). No. of bitstreams: 1 RAFAEL SOUZA BONIFÁCIO.pdf: 1138929 bytes, checksum: 39a4b1bda2dfd94d3eea7bbd3c234fc3 (MD5) Previous issue date: 2017-03-22 / The object of this dissertation is the writing in Avalovara (2005), of Osman Lins. The characteristics of the work reflect the new way of making art, becoming a kind of enigma. The general objective is to draw perceptions of the construction of the work. The specific objectives are developed around uniform and unequifled readings of the palindromes, perceiving the effects of the narrative that circulate times in the textual artistic atemporality. Criticism of the literary text in Avalovara (2005) propounds supposed divergences from the recognition of the work as a single genre, for it mixes words and symbols in the same field. The supposed need to show something different makes this literary art a reflection of solitary life in society. The stories depart from the imaginary, being revealed in the signs, in the spaces of plural senses, such as Abel's love . The sign form is contained within the palindrome within the spiral. Its coverage is of elements made up of words, numbers, symbols. All used to highlight the signs of a glowing image of literary genre. The authors worked include Ana Luiza Andrade (2014); Hannah Arendt (2000); Gaston Bachelard (2000); Mikhail Bakhtin (1997); João Alexandre Barbosa (1974); Roland Barthes (1992; 1987); Walter Benjamin (1996); Henri Bergson (2006); Antonio Candido (2005); Gilles Deleuze (1999; 2005); Benedito Nunes (1995), among others. In this sense, the theoretical analysis of writing focuses on the configuration of discourse. Thus, the structures of composition of the narrative permeate the Greek theater, with the palindrome, characteristic of the third century BC. Completeness goes on towards the infinite, establishing the imaginary by the fragments, causing variation of focuses, spaces, temporalities and languages. / O objeto desta dissertação é a escritura em Avalovara (2005), de Osman Lins. As características da obra repercutem a maneira nova de fazer arte, configurando-se numa espécie de enigma. O objetivo geral é traçar percepções da construção da obra. Os objetivos específicos são desenvolvidos em torno de leituras uniformes e desuniformes dos palíndromos, percebendo os efeitos da narrativa que circulam tempos na atemporalidade artística textual. A crítica do texto literário em Avalovara (2005) propala supostas divergências do reconhecimento da obra como gênero único, pois mistura palavras e símbolos num mesmo campo. A suposta necessidade de transparecer algo diferente faz dessa arte literária reflexo da vida solitária em sociedade. As histórias partem do imaginário, sendo reveladas nos signos, nos espaços de sentidos plurais, como o amor de Abel . A forma sígnica está contida no palíndromo, dentro da espiral. Sua cobertura é de elementos feitos de palavras, números, símbolos. Tudo usado para destacar os signos de uma imagem fulgurante de gênero literário. Os autores trabalhados incluem Ana Luiza Andrade (2014); Hannah Arendt (2000); Gaston Bachelard (2000); Mikhail Bakhtin (1997); João Alexandre Barbosa (1974); Roland Barthes (1992; 1987); Walter Benjamin (1996); Henri Bergson (2006); Antonio Candido (2005); Gilles Deleuze (1999; 2005); Benedito Nunes (1995), entre outros. Nesse sentido, a análise teórica da escritura incide na configuração do discurso. Assim, as estruturas de composição da narrativa perpassam pelo teatro grego, com o palíndromo, característico do século III a.C. A completude segue rumo ao infinito, estabelecendo o imaginário pelos fragmentos, causando variação de focos, espaços, temporalidades e linguagens.

Les principaux sujets d'intérêt de cette thèse concerneront deux notions de la complexité d'un mot infini : la complexité abélienne et la complexité de permutation. La complexité abélienne a été étudiée durant les dernières décennies. La complexité de permutation est, elle, une forme de complexité des mots relativement nouvelle qui associe à chaque mot apériodique de manière naturelle une permutation infinie. Nous nous pencherons sur deux sujets dans le domaine de la complexité abélienne. Dans un premier temps, nous nous intéresserons à une notion abélienne de la maximal pattern complexity définie par T. Kamae. Deuxièmement, nous analyserons une limite supérieure de cette complexité pour les mots C-équilibré. Dans le domaine de la complexité de permutation des mots apériodiques binaires, nous établissons une formule pour la complexité de permutation du mot de Thue-Morse, conjecturée par Makarov, en étudiant la combinatoire des sous-permutations sous l'action du morphisme de Thue-Morse. Par la suite, nous donnons une méthode générale pour calculer la complexité de permutation de l'image de certains mots sous l'application du morphisme du doublement des lettres. Finalement, nous déterminons la complexité de permutation de l'image du mot de Thue-Morse et d'un mot Sturmien sous l'application du morphisme du doublement des lettres. / The main topics of interest in this thesis will be two types of complexity, abelian complexity and permutation complexity. Abelian complexity has been investigated over the past decades. Permutation complexity is a relatively new type of word complexity which investigates lexicographical ordering of shifts of an aperiodic word. We will investigate two topics in the area of abelian complexity. Firstly we will consider an abelian variation of maximal pattern complexity. Secondly we consider an upper bound for words with the C-balance property. In the area of permutation complexity, we compute the permutation complexity function for a number of words. A formula for the complexity of Thue-Morse word is established by studying patterns in subpermutations and the action of the Thue-Morse morphism on the subpermutations. We then give a method to calculate the complexity of the image of certain words under the doubling map. The permutation complexity function of the image of the Thue-Morse word under the doubling map and the image of a Sturmian word under the doubling map are established.

Inverted repeats (IR) are common part of DNA of all living prokaryotic and eukaryotic organisms. Inverted repeats plays an important role in the regulation of basics cells processes. They are responsible for formation of cruciform structures. Inverted repeats also cause genomic instability and can be a source of numerous mutations. Cruciform structures can be recognized by DNA-binding proteins and can also act as a transcriptional regulators. Using the Palindrome Analyser tool, the frequency of IR and localization of inverted repeats in bacterial genomes was analyzed. The frequency of IR across the bacterial genome is variable. The frequency of short inverted repeats shows an approximately quadratic dependence on the %GC content in the genome with a minimum of about 50% of GC content. The localization of inverted repeats with respect to “annotated features” show a non-random distribution. The frequency of IR for most features is higher “outside” than “inside”.

Genetic information of all living organisms is stored in DNA. Exploring of its structure and function represents an important area of research in modern biology. One of the interesting structures occurring in DNA are palindromes. Based on the research they are expected to play an important role in interpreting the information stored in DNA, because they are often observed near important genes. Palindromes searching is complicated by the presence of mutations (changes in sequences of DNA elements), which increases the time complexity of algorithms. Therefore it is reasonable to study their parallelization and acceleration. The objective of this work is a study of palindromes searching methods and acceleration architecture design. The hardware unit implemented in a chip with FPGA technology placed on ml555 board can speed up the calculation up to 6 667 times in comparison with the best-known software method relying on suffix arrays.

Nikolai Medtner's works evidence an intense interest in symmetrical designs. This concern is manifest at all levels, from the large scale proportions of his numerous ingenious sonata forms to the symmetrically constructed themes and motives. Medtner's works include several instances of palindromic themes and periods. Some palindromic contours are achieved through immediate inversion, creating expansive, symmetrical waves. One of Medtner's thumbprints, symmetrical contrary voice-leading, consists of two or more voices which systematically expand or contract in exact mirror fashion. The contrary movement is usually stepwise, and may be either chromatic or diatonic. Occasionally even larger intervals, such as thirds and fourths, are subjected to this favourite mirroring technique. Such symmetrical expansion and contraction often controls the harmonic progression of several consecutive bars. One of the most striking aspects of Medtner's music is his sophisticated harmonic language. He was fascinated with symmetrical harmonic designs, such as the tritone, the French sixth chord, and the octatonic scale, and made endless and increasingly intricate explorations into these stuctures and the ways in which these apparently nontonal, non-hierarchical forms could be coordinated with the fundamental hierarchy of asymmetrical tonal forms, including triads, major and minor scales, and tonic-dominant relations. Medtner's late work, the Grozovaya Sonata, Opus 53 No.2, is the most concentrated and abstract of his works. The themes are built from highly lapidar motives, giving this work an intensely angular, rigorously mathematical character. All the symmetrical hallmarks of Medtner's language are in abundant evidence in this great work. Features include the extensive symmetrical mirroring of the opening section, frequent use of contrary voice leading as a generator of harmonic progression, and constant tritone shifting. Medtner also builds sequential chains based on two more symmetrical forms, the diminished seventh and the augmented triad. Finally, the design of this unique single movement sonata may be a hybrid of sonata form with palindrome. The Grozovaya Sonata is a microcosm of the symmetrical features of Medtner's language.

<p>In the thesis we are concerned with actual problems on palindromic subwords and palindromic factors of finite and infinite words. The main course of the research are the ways of determining which of two given words is &ldquo;more palindromic&rdquo; than the other one, that is, defining a measure for the degree of &ldquo;palindromicity&rdquo; of a word. Particularly, we pay attention to two actual approaches: the so-called MP-ratio and the so-called <em>palindromic defect</em>, and answer several open questions about them.<br /><br />Namely, concerning the MP-ratio, a few plausible-looking question have been asked in the literature, which would have, if answered positively, made computations of MP-ratios significantly simpler. We add one more related question to these ones, and then show that, rather unexpectedly, all these questions have negative answer.<br /><br />Concerning the palindromic defect, the main result of this work is a construction of an infinite class of infinite words that have several properties that were sought after in some recent works in this area. Among the most interesting facts is that that all these words are aperiodic words of a finite positive defect, having the set of factors closed under reversal---in some recent works, the construction of even a single word having these properties turned out to be quite hard. Using these words, which we are calling <em>highly potential words</em>, we check the validity of several open&nbsp; conjectures, and for several of them we find out that they are false.</p> / <p> U tezi razmatramo aktuelne probleme u vezi s palindromskim podrečima i palindromskim faktorima konačnih i beskonačnih reči. Glavni pravac istraživanja jesu kriterijumi za određivanje koja od dve date reči je &bdquo;palindromičnija&ldquo; od druge, tj. određivanje stepena &bdquo;palindromičnosti&ldquo; date reči. Akcenat stavljamo na dva aktuelna pristupa: tzv. <em>MP-razmeru</em> i tzv. <em>palindromski defekt</em>, i odgovaramo na vi&scaron;e otvorenih pitanja u vezi s njima.<br /> <br /> Naime, u vezi sa MP-razmerom u literaturi je postavljeno vi&scaron;e pitanja, intuitivno uverljivih, koja bi, u slučaju pozitivnog razre&scaron;enja, znatno pojednostavila izračunavanje MP-razmere. Ovim pitanjima dodajemo jo&scaron; jedno srodno, a zatim pokazujemo da, prilično neočekivano, sva ova pitanja imaju negativan odgovor.<br /> <br /> U vezi s palindromskim defektom, glavni rezultat rada je konstrukcija beskonačne klase beskonačnih reči koje imaju vi&scaron;e osobina za kojima je iskazana potreba u skora&scaron;njim radovima iz ove oblasti. Među najzanimljivije spada činjenica da su sve aperiodične reči konačnog pozitivnog defekta, i da im je skup faktora zatvoren za preokretanje &ndash; u nekim skora&scaron;njim radovima konstrukcija makar jedne reči s ovim osobinama pokazala se kao prilično te&scaron;ka. Pomoću ovih reči, koje nazivamo <em>visokopotencijalne reči</em>, ispitujemo validnost vi&scaron;e otvorenih hipoteza, i za vi&scaron;e njih ustanovljavamo da nisu validne.</p>

<p>We focus on two complexity measures of words that are invariant under the operation of reversal of a word: the palindromic defect and the MP-ratio.The palindromic defect of a given word w is dened by jwj + 1&nbsp;&nbsp; jPal(w)j, where jPal(w)j denotes the number of palindromic factors of w. We study innite words, to which this de&nbsp; nition can be naturally extended. There are many results in the literature about the so- called rich words (words&nbsp; of defect 0), while words of nite positive defect have been studied signicantly less; for some time (until recently) it was not known whether there even exist such words that additionally are aperiodic and have their set of factors closed under reversal. Among the rst examples that appeared were the so-called highly potential words. In this&nbsp; thesis we present a much more general construction,which gives a wider class of words, named generalized highly potential words, and analyze their signicance within the frames of combinatorics on words.The MP-ratio of a given n-ary&nbsp; word w is dened as the quotient jrwsj jwj ,where r and s are words such that the word rws is minimal- palindromic and that the length jrj + jsj is minimal possible; here, an n-ary word is called minimal-palindromic if it does not contain palindromic subwords of length greater than jwj n . In the binary case, it was proved that the MP-ratio is well-dened and that it is bounded from above by 4, which is the best possible upper bound. The question of well- denedness of the MP-ratio for larger alphabets was left open. In this thesis we solve that&nbsp; question in the ternary case: we show that the MP-ratio is indeed well-dened in the ternary case, that it is bounded from above by the constant 6 and that this is the best possible upper bound.</p> / <p>Izucavamo dve mere slozenosti reci koje su invarijantne u odnosu na operaciju preokretanja reci: palindromski defekt i MP-razmeru date reci.Palindromski defekt reci w denise se kao jwj + 1&nbsp;&nbsp; jPal(w)j, gde jPal(w)j predstavlja broj palindromskih faktora reci w. Mi izucavamo beskonacne reci, na koje se ova denicija moze prirodno prosiriti. Postoje mnogobrojni rezultati u vezi sa tzv. bogatim recima (reci cije je defekt 0), dok se o recima sa konacnim pozitivnim defektom relativno malo zna; tokom jednog perioda (donedavno) nije bilo poznato ni da li uopste postoje takve reci koje su,dodatno, aperiodi cne i imaju skup faktora zatvoren za preokretanje. Medu prvim primerima koji su se pojavili u literaturi su bile tzv. visokopotencijalne reci. U disertaciji cemo predstaviti znatno opstiju konstrukciju, kojom se dobija znacajno sira klasa reci, nazvanih uop stene visokopotencijalne reci, i analiziracemo njihov znacaj u okvirima kombinatorike na recima.MP-razmera date n-arne reci w denise se kao kolicnik jrwsj jwj , gde su r i s takve da je rec rws minimalno-palindromicna, i duzina jrj + jsj je najmanja moguca; ovde, za n-arnu rec kazemo da je minimalno-palindromicna ako ne sadrzi palindromsku podrec duzine vece od&nbsp; jwj n&nbsp; . U binarnom slucaju dokazano je da je MP-razmera dobro&nbsp; denisana i da je ogranicena odozgo konstantom 4, sto je i najbolja moguca granica. Dobra denisanost MP-razmere za vece alfabete je ostavljena kao otvoren problem. U ovoj tezi resavamo taj problem u ternarnom slucaju: pokazacemo da MP- razmera jeste dobro de-nisana u ternarnom slucaju, da je ogranicena odozgo sa 6, i da se ta granica ne moze poboljsati.<br />&nbsp;</p>

No description available.