Polimorfismos do tipo indel são os mais abundantes depois dos SNPs, representando 3,6 milhões das variantes caracterizadas pelo projeto 1000 Genomes. Com uma distribuição que pode ser estimada em mais de um indel a cada 1000 pb, são facilmente encontrados em regiões de interesse. A baixa taxa de mutação e a possibilidade de desenhar primers alelo-específicos são as principais características dos indels que os diferenciam de STRs. O uso de primers aleloespecíficos na detecção e dosagem de misturas de DNA apresenta maior sensibilidade e acurácia que as técnicas usualmente empregadas. Aqui foram descritos, para 10 lócus indel, pares de primers flanqueadores e alelo-específicos para ambos os alelos (inserção e deleção) e foi realizado o estudo populacional em 160 indivíduos. A determinação de fenótipos e avaliação de especificidade dos primers, dos quais 28 foram específicos, foi realizada por PCR convencional seguida de PAGE. As análises populacionais e forenses mostraram que esses lócus apresentam alta variabilidade (heterozigose de 30-50%) e consequentemente, alta informatividade. Os valores de PIC, PE e PD variaram de 0,2763 a 0,3750; 0,1381 a 0,1875 e 0,4978 a 0,6250 respectivamente. Os valores cumulativos de PCE e PCD foram respectivamente 0,8508 e 0,9999. Assim, esse conjunto de indels é indicado para serem testados na detecção e quantificação de misturas de DNA a partir da amplificação alelo-específica. / Indels polymorphisms are the most abundant after SNPs, representing 3.6 million of the variants characterized by the 1000 Genomes project. With a distribution that can be estimated at more than one indel per 1000 bp, they are easily found in regions of interest. The low mutation rate and the possibility of designing allele-specific primers are the main characteristics of the indels that differentiate them from STRs. The use of allele-specific primers in the detection and dosage of DNA mixtures is more sensitive and accurate than regularly employed techniques. Here, for 10 indel loci, pairs of flanking primers and allele-specific primers, for both alleles (insertion and deletion), were described and a population study was performed on 160 individuals. Determining phenotypes and evaluation of primers specificity, of which 28 were specific, was performed by conventional PCR followed by PAGE. In population and forensic analysis, these loci showed high variability (heterozygosis of 30-50%) and consequently high informativeness. The values of PIC, PE and PD ranged from 0.2763 to 0.3750, 0.1381 to 0.1875 and 0.49978 to 0.6250 respectively. Combined values of PCE and PCD were respectively 0.8508 and 0.9999. Thus, this set of indels is indicated to be tested for detection and quantification of DNA mixtures using the allele-specific amplification method.

DE LA TESIS:La noción de "ideal primo" (Dedekind 1871) ha ido adquiriendo cada vez mayor importancia hasta ocupar, con la Teoría de Esquemas de Grothendieck el centro mismo del Algebra Conmutativa. El estudio de los anillos conmutativos se convierte así en el de los esquemas afines con base en espacios topológicos que son el espectro primo de un anillo conmutativo, correspondiéndose funtorialmente los homomorfismos de anillos A->B con morfismos de esquemas que inducen en los espacios base las aplicaciones continuas Spec B -> Spec A. Un responsable fundamental en una parte de esta evolución es W. Krull (1899-1971). Señalemos algunos aspectos de su contribución únicamente desde el punto de vista de nuestro trabajo. A Krull se debe (en 1926) la definición de dimensión de un anillo como supremo de las longitudes de las cadenas de ideales primos de A asociando por primera vez el objeto geométrico Spec A al objeto algebraico A. Su famoso "Hauptidealsatz" hace que, en palabras de Northcott un anillo noetheriano deje de ser un pálido reflejo de un anillo de polinomios y convierte al conjunto ordenado Spec A en algo semejante al conjunto de subvariedades irreducibles de una variedad algebraica afín Spec A verifica la condición de cadena descendente en un sentido fuerte la altura de un ideal primo es finita entre dos ideales primos comparables no adyacentes existen infinitos ideales primos, etc. Más tarde Krull demuestra que si A es un anillo local regular h(P)+ch(P)=dim A para todo P Spec A Pasamos a describir el contenido de la memoria en términos generales Un complemento de esta descripción son las introducciones a los tres capítulos de que consta así como los comenta nos intercalados en ellos. Se ha preferido prescindir de capítulo 0 y de enunciados de definiciones y resultados conocidos, salvo en contadas ocasiones bien especificadas. A cambio se citan con precisión todos los datos utilizados a riesgo de ser a veces un poco prolijos. El estudio de la propiedad de going-between ocupa los capítulos II y III de nuestra memoria El capítulo I es independiente de dicha propiedad y tiene como fin básico el cálculo de la dimensión de Krull en una extensión de anillos. Parte de los resultados son utilizados luego en los dos capítulos posteriores pero creemos que primordialmente son de interés por sí mismos. La motivación principal está en conseguir para una extensión ACB de anillos íntegros fórmulas que relacionen dim B con dim A y gr tr (A)B en las condiciones mas generales posibles. Tales fórmulas existen en la literatura solo cuando B es un anillo de polinomios ó una extensión entera aparte del clásico caso de las álgebras afines sobre un cuerpo El objetivo se logra de hecho de forma óptima con la única restricción de que A sea un anillo noetheriano.Se comienza el capítulo I introduciendo lo que hemos llamado radical dimensional de un anillo y dando métodos de calculo de dicho ideal y también de la intersección de ciertas familias de idea les primos de un anillo noetheriano relacionadas con la dimensión. El radical dimensional aparece luego como la obstrucción a que la dimensión de Krull pueda expresarse para un anillo noetheriano cualquiera en términos del grado de trascendencia como ocurre con las álgebras afines sobre un cuerpo. En el capítulo II se comienza el estudio de la propiedad de "going-between". Se define lo que llamamos GB-extensión A C B es una GB-extensión si la aplicación Spec B -> Spec A tiene la propiedad de "going-between". Tras el examen de las generalidades del caso se centra el interés en la relación entre GB-extensiones y las más simples GD-extensiones, definidas relativamente a la propiedad de "going-down". Se observa el papel de puente que van a jugar en ello los anillos de valoración a causa de la simplicidad de su espectro. El capítulo III presenta los resultados de mayor interés (y sin duda los más complejos) en torno a la propiedad de "going-between". Se trata en definitiva de averiguar qué anillos noetherianos son GB(2)-anillos lamentablemente la condición se revela muy restrictiva por encima de la dimensión 3. Se abordan con diferentes métodos dos casos fundamentales anillos que son álgebras finitogeneradas y anillos de series formales. Resulta obligado explicar la disparidad de los métodos empleados en las dos partes del capítulo III. La condición necesaria (III 1-1) es en principio de generalidad total, pero plantea a su vez un difícil problema (conjetura de Kaplansky-Hochster) cuando se puede asegurar que dos ideales primos de altura 2 contienen simultáneamente algún ideal primo de altura 1. Aunque en ciertos casos geométricos el problema aparece como "naif", existen contraejemplos al caso general y de hecho sólo recientemente se tienen datos positivos en anillos de polinomios (McAdam). Esto explica el largo y paciente peregrinaje que representan las demostraciones de las proposiciones (III 1-4) y (III 1-6) antes mencionadas y la forma de sus enunciados. Asimismo pone de manifiesto que el método no es aplicable a los anillos de series. Finalmente digamos que los resultados obtenidos hacen pensar como improbable la existencia de GB(2)-anillos noetherianos de dimensión superior a 3 e incluso en éste último caso, un GB(2)-anillo aparece como algo muy semejante a un anillo henseliano.

The thesis is focused on the Nueva Coronica y Buen Gobierno, by Felipe Guaman Poma de Ayala, written in the Peruvian highlands between the end of the sixteenth and the beginning of the seventeenth centuries. Although specifically designed to superficially appear innocuously and mildly complaining, the author disguises his transcendental subversive intentions by limiting the scope of the referential subject to the members of his cultural group. / While the introduction explains in detail the objective of the thesis and reviews some literature on the subject, the first chapter provides a broad and summary overview of indigenous Andean cosmology, its constitutive elements and its main characteristics. In the second chapter these elements of cosmological philosophy are presented as the only available tools at the disposal of the indigenous population in order to understand that catastrophic event referred to as the Conquest and the inevitable conclusion to which it arrived. The third chapter explores the use of those cosmological tools and the understanding of the disaster in the subversive endeavour of cultural survival in the context of colonization. Finally, the fourth chapter examines the plurality of levels of subversive messages conveyed by the author and his hidden message of rebellious hope. Within the same frame of cosmologically oriented thought patterns and messianistic expectations, Guaman Poma alters one apparently insignificant historical detail, thereby making possible the cosmic regeneration and historical rebirth of the last Inca emperor and his entire people. A section of conclusions and a bibliography follow the fourth and last chapter.

DNA polymerase epsilon (Pol ε) is a multi-subunit B-family DNA polymerase that is involved in leading strand DNA replication in eukaryotes. DNA Pol ε in yeast consists of four subunits, Pol2, Dpb2, Dpb3, and Dpb4. Pol2 is the catalytic subunit and Dpb2, Dpb3, and Dpb4 are the accessory subunits. Pol2 can be further divided into an N-terminal catalytic core (Pol2core) containing both the polymerase and exonuclease active sites and a C-terminus domain. We determined the X-ray crystal structure of Pol2core at 2.2 Å bound to DNA and with an incoming dATP. Pol ε has typical fingers, palm, thumb, exonuclease, and N-terminal domains in common with all other B-family DNA polymerases. However, we also identified a seemingly novel domain we named the P-domain that only appears to be present in Pol ε. This domain partially encircles the nascent duplex DNA as it leaves the active site and contributes to the high intrinsic processivity of Pol ε. To ask if the crystal structure of Pol2core can serve as a model for catalysis by Pol ε, we investigated how the C-terminus of Pol2 and the accessory subunits of Pol ε influence the enzymatic mechanism by which Pol ε builds new DNA efficiently and with high fidelity. Pre-steady state kinetics revealed that the exonuclease and polymerization rates were comparable between Pol2core and Pol ε. However, a global fit of the data over five nucleotide-incorporation events revealed that Pol ε is slightly more processive than Pol2 core. The largest differences were observed when measuring the time for loading the polymerase onto a 3' primer-terminus and the subsequent incorporation of one nucleotide. We found that Pol ε needed less than a second to incorporate the first nucleotide, but it took several seconds for Pol2core to incorporate similar amounts of the first nucleotide. B-family polymerases have evolved an extended β-hairpin loop that is important for switching the primer terminus between the polymerase and exonuclease active sites. The high-resolution structure of Pol2core revealed that Pol ε does not possess an extended β-hairpin loop. Here, we show that Pol ε can processively transfer a mismatched 3' primer-terminus between the polymerase and exonuclease active sites despite the absence of a β-hairpin loop. Additionally we have characterized a series of amino acid substitutions in Pol ε that lead to altered partitioning of the 3'primer-terminus between the two active sites. In a final set of experiments, we investigated the ability of Pol ε to displace the downstream double-stranded DNA while carrying out DNA synthesis. Pol ε displaced only one base pair when encountering double-stranded DNA after filling a gap or a nick. However, exonuclease deficient Pol ε carries out robust strand displacement synthesis and can reach the end of the templates tested here. Similarly, an abasic site or a ribonucleotide on the 5'-end of the downstream primer was efficiently displaced but still only by one nucleotide. However, a flap on the 5'-end of the blocking primer resembling a D-loop inhibited Pol ε before it could reach the double-stranded junction. Our results are in agreement with the possible involvement of Pol ε in short-patch base excision repair and ribonucleotide excision repair but not in D-loop extension or long-patch base excision repair.

THESIS SUMMARY:BACKGROUND: Abnormal ductus venosus flow at 11-13 weeks has been associated to fetal chromosomal abnormalities and cardiac defects.The hypothesis of the studies is that flow through the ductus venosus can be assessed routinely at 11-13 weeks of gestation and that abnormal flow at this scan can help identify fetal chromosomal and structural defects as well as adverse pregnancy outcome.STUDIES:In the first study, ten sonographers received practical training in accurate assessment of the ductus venosus and performed 300 examinations each. The sonographers required an average of 80 examinations before they could successfully examine the ductus venosus flow. In the second study ductus venosus flow was assessed immediately before chorion villous sampling (CVS) in fetuses with nuchal translucency (NT) thickness of 3.5 mm or more. A fetal echocardiography was performed in euploid fetuses at 11-13 weeks and/or 18-22 weeks. Reverse or absent flow during atrial contraction was observed in 68.8% of the fetuses with cardiac defects and in 22.9% with no cardiac defects. In the third study screening by the combined test was performed in singleton pregnancies, including 19,614 with euploid fetuses, 122 with trisomy 21, 36 with trisomy 18, 20 with trisomy 13 and 8 with Turner syndrome. We examined the performance of two screening strategies: firstly, assessment of the a-wave in all patients and secondly, first-stage screening using the combined test in all patients followed by second-stage assessment of the a-wave only in those with an intermediate risk of 1 in 51 to 1 in 1,000 after the first-stage. Reversed a-wave was observed in 3.2% of the euploid fetuses and in 66.4%, 58.3%, 55.0% and 75.0% of fetuses with trisomies 21, 18 and 13 and Turner syndrome, respectively. Inclusion of ductus venosus flow in all pregnancies would detect 96%, 92%, 100% and 100% of trisomies 21, 18 and 13 and Turner syndrome, respectively, at a false positive rate of 3%. The same detection rates were achieved with the two-stage strategy at a false positive rate of 2.6%.In the fourth study the patients were subdivided into five groups: normal outcome (n=10,120), miscarriage or fetal death (n=185), abnormal karyotype (n=95), major cardiac (n=20) or non-cardiac defect (n=70). The prevalence of reversed a-wave was significantly higher in the groups with miscarriage or fetal death (10.8%), abnormal karyotype (62.1%) and fetal cardiac defect (25.0%) but not non-cardiac defect (4.3%) than in the normal outcome group (3.7%). The fifth study was a prospective study in 516 dichorionic and 179 monochorionic twin pregnancies. The prevalence of reversed a-wave in the fetal ductus venosus was compared between monochorionic and dichorionic pregnancies and between those with and without pregnancy complications. The prevalence of reversed a-wave in at least one of the fetuses was significantly higher in monochorionic than in dichorionic pregnancies (18.4% vs. 8.3%, p<0.001) and in pregnancies complicated by miscarriage (28.6%, p=0.005), fetal aneuploidy (70.0%, p<0.001) and twin-to-twin-transfusion syndrome (TTTS) (38.5%, p<0.001) compared to the pregnancies with two healthy live births (7.7%). Pregnancy outcome was normal in 76.7% dichorionic and in 42.4% monochorionic twins with reversed a-wave in at least one of the fetuses.CONCLUSIONS: After an extensive supervised training, ductus venosus flow assessment can be incorporated into the first trimester scan, where it improves the performance of screening for chromosomal defects and cardiac defects, and it helps to identify the fetuses with a higher risk of death. Similarly, in twin pregnancies ductus venosus assessment identifies the pregnancies with a higher risk of having a fetus with an aneuploidy, those with a higher risk of miscarriage, and those that will subsequently develop TTTS.KEY WORDS: Ductus venosus, First trimester, Chromosomal abnormality, Cardiac effect, Adverse outcome, Twin pregnancy

Resumo: Formigas cortadeiras do gênero Atta, popularmente conhecidas como saúvas, são as mais derivadas dentro da tribo Attini. Apresentam grande importância ecológica, porém, pelo hábito de cortarem folhas para manutenção do fungo simbionte e pelo enorme tamanho das colônias, causam muitos prejuízos às lavouras, pastagens e plantações, sendo consideradas pragas agrícolas. Atta laevigata Smith, 1858 apresenta vasta distribuição pelo Brasil e é responsável pela herbivoria de inúmeras plantas dicotiledôneas, gramíneas e espécies nativas de diferentes biomas. O presente trabalho teve como objetivos a caracterização parcial do transcriptoma e do genoma mitocondrial de A. laevigata. Foram caracterizadas 2006 sequências únicas do transcriptoma, a partir de uma biblioteca de cDNA preparada com indivíduos inteiros da formiga. Entre essas sequências, 16 provavelmente representam genes com grande número de transcritos. Esses 16 genes estão relacionados a três funções celulares: (i) conservação de energia através de reações redox na mitocôndria; (ii) estrutural, pelo citoesqueleto e músculos; (iii) regulação da expressão gênica e metabolismo. Considerando o estilo de vida e processos biológicos chaves para essas formigas, 146 sequências foram identificadas com base na sua utilização para o controle de cortadeiras pragas. A partir de dados da biblioteca de cDNA e procedimentos envolvendo primer walking, o genoma mitocondrial de A. laevigata foi parcialmente caracterizado, apresentandose com 17920 pb, maior, portanto, do que outros já descritos em Hymenoptera, mesmo considerando-se a impossibilidade de determinação da sequência de uma pequena porção do mtDNA, envolvendo a região controle, uma parte do 12S e os tRNAs S1, V e M. Como já descrito para outros mitogenomas, o de A. laevigata apresentou alto conteúdo AT, os mesmos 13 genes codificadores... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Leafcutter ants from Atta genus, popularly known as "saúvas", are the most derived of the tribe Attini. They have major ecological importance, but, because of their habit of cutting leaves for the maintenance of the symbiotic fungus and the huge colony size, they impose severe economic damages to plantations, pastures, and agriculture, being considered as agriculture pests. Atta laevigata shows wide distribution in Brazil and it is responsible for the herbivory of many dicots, grass, and native species from different biomes. The present work aimed to characterize the transcriptome and the mitochondrial genome of A. laevigata. 2,006 unique sequences of the transcriptome were characterized from a cDNA library constructed with whole individuals. Among those sequences, 16 are likely from genes with high number of transcripts. Those 16 genes are related with three cellular functions: (i) energy conservation through redox reactions in mitochondria; (ii) cytoskeleton and muscle structuring; (iii) regulation of gene expression and metabolism. Based on lifestyle and key biological processes of these ants, 146 sequences were identified with potential use for controlling pest leafcutters. Using data from cDNA library and primer walking proceedings, the mitochondrial genome of A. laevigata was partially characterized with 17,920 bp, being larger than the others already described for Hymenoptera. A small part of the mtDNA was not sequenced, including the control region, a portion of 12S and tRNAs S1, V, and M. As described before for other mitogenomes, A. laevigata mtDNA displayed high AT contain, the same 13 proteincoding genes and the two ribosomal subunits with length and location according to the hypothetic ancestral mitogenome. Rearrangements were found for the tRNAs, but the most remarkable difference were the high number and longer length of intergenic regions presented in the mtDNA... (Complete abstract click electronic access below) / Orientador: Maurício Bacci Júnior / Coorientador: Henrique Ferreira / Banca: Flavio Henrique da Silva / Banca: Marco Antonio del Lama / Banca: Mariana Lúcio Lyra / Banca: Klaus Hartmann Hartfelder / Doutor

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The successful completion of the Hiten mission in 1991 provided real-world validation of a class of trajectories defined as ballistic lunar capture transfers. This class of transfers is often considered for missions to the Moon and for tours of the moons of other planets. In this study, the dynamics of the three and four body problems are examined to better explain the mechanisms of low energy transfers in the Earth-Moon system, and to determine their optimality. Families of periodic orbits in the restricted Earth-Sun-spacecraft three body problem are shown to be generating families for low energy transfers between orbits of the Earth. The low energy orbit-to-orbit transfers are shown to require less fuel than optimal direct transfers between the same orbits in the Earth-Sun-spacecraft circular restricted three body problem. The low energy transfers are categorized based on their generating family and the number of flybys in the reference three body trajectory. The practical application of these generating families to spacecraft mission design is demonstrated through a robust nonlinear targeting algorithm for finding Sun-Earth- Moon-spacecraft four body transfers based on startup transfers indentified in the Earth- Sun three body problem. The local optimality of the transfers is examined through use of Lawden’s primer vector theory, and new conditions of optimality for single-impulse-to-capture lunar transfers are established. / text

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