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ABSTRACT Background: Palindromic rheumatism (PR) is the rare disease that generally occurs with multiple recurring attacks of painful inflammation affecting joints and adjacent tissues. The thesis attempts to characterize the association in 10 instances of the single nucleotide polymorphisms (SNPs) of tumor necrosis factor genes (TNF-£\, TNFRSF1A and TNFRSF1B), Interleukin-1£] genes and Palindromic rheumatism (PR). Methods: The genetic polymorphisms of TNF-£\, TNFR£L, TNFR£S and IL-1£] genes cluster were investigated among 56 PR patients identified from the Kaohsiung Veterans General Hospital (VGHKS, Kaohsiung, Taiwan) and compared with one hundred healthy subjects. The genotypes for ten SNPs in the TNF-£\, TNFRSF1A, TNFRSF1B and IL-1£] genes among these 156 individuals were examined. Results: Experiments indicate significant count of the TNFRSF1A+36 AG genotype in PR patients (OR=4.8, 95%CI=1.8-13.0, p=0.002) and TNFRSF1A+36G allele (OR=3.94, 95%CI=1.59-9.79, p=0.003).The results also have remarkable correlation with TNFRSF1B haplotype +676/+1663 T/A (OR=2.12, CI=1.2-3.8, p=0.010). However, on significant differences were found for all the TNF-£\and IL-1£]polymorphisms. Conclusions: Genetic polymorphisms in TNF-£\ receptors are associated with susceptibility and severity of the inflammatory response in the PR patients.

DNA repetitive sequences capable of adopting non-B DNA structures are a potent source of instability in eukaryotic genomes. They are strong inducers of chromosomal fragility and genome rearrangements that cause various hereditary diseases and cancers. In addition, a subset of repeats also has an ability to expand, which leads to more than 20 human genetic diseases that are collectively known as repeat expansion diseases. However, the mechanisms underlying the potential of these structure-prone motifs to break and expand are largely unknown. In this study, a systematic genome-wide screen was employed in yeast Saccharomyces cerevisiae to investigate the contributing factors of the instability of two representative non-B DNA-forming repeats: the triplex-adopting GAA/TTC tracts and the inverted repeats that can form hairpin and cruciform structures. The GAA/TTC screen revealed that DNA replication and transcription initiation are the two major pathways governing the GAA/TTC stability in yeast, as corresponding mutants strongly induce both fragility and large-scale expansions of the repeats. The inverted repeats screen and follow-up experiments revealed that both replication-dependent and -independent pathways are involved in maintaining the stability of palindromic sequences. We propose that similar mechanisms could operate in the human cells to mediate the deleterious metabolism of GAA and inverted repeats.

Chromosomal rearrangements play a major role in the evolution of eukaryotic genomes. Genomic aberrations are also a hallmark of many tumors and are associated with a number of hereditary diseases in humans. The presence of repetitive sequences that can adopt non-canonical DNA structures is one of the factors which can predispose chromosomal regions where they reside to instability. Palindromic sequences (inverted repeats with or without a unique sequence between them) that can adopt hairpin or cruciform structures are frequently found in regions that are prone for gross chromosomal rearrangements (GCRs) in somatic and germ cells in different organisms. Direct physical evidence was obtained that double-strand breaks (DSBs) occur at the location of long inverted repeats, a triggering event for the genomic instability. However, the mechanisms by which palindromic sequences lead to chromosomal fragility are largely unknown. The overall goal of this research is to elucidate the mechanisms of DSB and GCR generation by palindromic sequences in yeast, Saccharomyces cerevisiae.

Submitted by Eloiza do Nascimento Fazinazzo null (elofazinazzo@hotmail.com) on 2016-09-12T20:02:28Z No. of bitstreams: 1 EloizaNFazinazzo_Dissertação.pdf: 2610907 bytes, checksum: 0d329afcf9d2ecddb98957de37f5ba97 (MD5) / Approved for entry into archive by Felipe Augusto Arakaki (arakaki@reitoria.unesp.br) on 2016-09-14T19:35:27Z (GMT) No. of bitstreams: 1 fazinazzo_en_me_prud.pdf: 2610907 bytes, checksum: 0d329afcf9d2ecddb98957de37f5ba97 (MD5) / Made available in DSpace on 2016-09-14T19:35:27Z (GMT). No. of bitstreams: 1 fazinazzo_en_me_prud.pdf: 2610907 bytes, checksum: 0d329afcf9d2ecddb98957de37f5ba97 (MD5) Previous issue date: 2016-07-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Neste trabalho foi realizado um estudo sobre o comportamento dos zeros de polinômios palindrômicos, com foco nos zeros reais. Condições necessárias e suficientes para que um polinômio palindrômico com coeficientes reais tenha somente zeros reais são estabelecidas. / In this work is presented a study of the behavior of the zeros of palindromic polynomials, focusing on real zeros. Necessary and sufficient conditions for a palindromic polynomial with real coefficients has only real zeros are established. / FAPESP: 2014/06785-2

<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.

In recent years, combinatorial properties of finite and infinite words have become increasingly important in fields of physics, biology, mathematics, and computer science. In particular, the fascinating family of Sturmian words has become an extremely active subject of research. These infinite binary sequences have numerous applications in various fields of mathematics, such as symbolic dynamics, the study of continued fraction expansion, and also in some domains of physics ( quasicrystal modelling ) and computer science ( pattern recognition, digital straightness ). There has also been a recent surge of interest in a natural generalization of Sturmian words to more than two letters - the so - called episturmian words, which include the well - known Arnoux - Rauzy sequences. This thesis represents a significant contribution to the study of Sturmian and episturmian words, and related objects such as generalized Thue - Morse words and substitutions on a finite alphabet. Specifically, we prove some new properties of certain palindromic factors of the infinite Fibonacci word; establish generalized ' singular ' decompositions of suffixes of certain morphic Sturmian words; completely describe where palindromes occur in characteristic Sturmian words; explicitly determine all integer powers occurring in a certain class of k-strict episturmian words ( including the k-bonacci word ) ; and prove that certain episturmian and generalized Thue - Morse continued fractions are transcendental. Lastly, we begin working towards a proof of a characterization of invertible substitutions on a finite alphabet, which generalizes the fact that invertible substitutions on two letters are exactly the Sturmian morphisms. / Thesis (Ph.D.)--School of Mathematical Sciences, 2006.

Yogurt is a characteristic fermented dairy product of Turkey and Bulgaria and its popularity has been increasing all over the world. Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus (Lactobacillus bulgaricus) are used together as starter culture in production of yogurt. The objective of this study was to isolate and characterize yogurt cultures from traditionally produced yogurts (i.e. produced without using commercial starter cultures) and to search the genotypic diversity within traditional S. thermophilus isolates. Yogurt cultures were isolated from traditionally produced yogurts collected from different regions of Turkey and identified biochemically. Acidification ability of the isolates was examined and the cultures giving best acidifying rates were further subjected to a selection in terms of their acetaldehyde production ability. Then, phage resistance and proteolytic activity of chosen isolates were tested. Finally, twenty-five L. bulgaricus and twenty-two S. thermophilus isolates were selected as cultures having best technological properties. Furthermore, subtyping studies were carried out to indicate strain diversity among isolates. S. thermophilus was selected as target organism for subtyping in this study. Clustered regularly interspaced short palindromic repeats (CRISPR) loci are highly polymorphic genetic regions, which are composed of partially palindromic direct repeats interspaced by sequences called spacers. In order to characterize S. thermophilus isolates genotypically, CRISPR1 locus of the isolates were analyzed. Additionally, nineteen isolates selected after CRISPR1 analysis were characterized using multilocus sequence typing (MLST). This provided to compare CRISPR1 analysis with MLST as a typing method. According to CRISPR1 analysis S. thermophilus isolates were grouped into 6 main clusters with a total of 15 sub-clusters. MLST results demonstrated an evolutionary relationship among these strains compatible with that derived from the CRISPR1 analysis.