Genetic Analysis of Mitotic Recombination in Saccharomyces cerevisiae

Mitotic genome instability can occur during the repair of double-strand breaks (DSBs) in DNA, which arise from endogenous and exogenous sources. Studying the mechanisms of DNA repair in the budding yeast, Saccharomyces cerevisiae has shown that Homologous Recombination (HR) is a vital repair mechanism for DSBs. HR can result in a crossover event, in which the broken molecule reciprocally exchanges information with a homologous repair template. The current model of double-strand break repair (DSBR) also allows for a tract of information to non-reciprocally transfer from the template molecule to the broken molecule. These “gene conversion” events can vary in size and can occur in conjunction with a crossover event or in isolation. The frequency and size of gene conversions in isolation and gene conversions associated with crossing over has been a source of debate due to the variation in systems used to detect gene conversions and the context in which the gene conversions are measured.

In Chapter 2, I use an unbiased system that measures the frequency and size of gene conversion events, as well as the association of gene conversion events with crossing over between homologs in diploid yeast. We show mitotic gene conversions occur at a rate of 1.3x10-6 per cell division, are either large (median 54.0kb) or small (median 6.4kb), and are associated with crossing over 43% of the time.

DSBs can arise from endogenous cellular processes such as replication and transcription. Two important RNA/DNA hybrids are involved in replication and transcription: R-loops, which form when an RNA transcript base pairs with the DNA template and displaces the non-template DNA strand, and ribonucleotides embedded into DNA (rNMPs), which arise when replicative polymerase errors insert ribonucleotide instead of deoxyribonucleotide triphosphates. RNaseH1 (encoded by RNH1) and RNaseH2 (whose catalytic subunit is encoded by RNH201) both recognize and degrade the RNA in within R-loops while RNaseH2 alone recognizes, nicks, and initiates removal of rNMPs embedded into DNA. Due to their redundant abilities to act on RNA:DNA hybrids, aberrant removal of rNMPs from DNA has been thought to lead to genome instability in an rnh201Δ background.

In Chapter 3, I characterize (1) non-selective genome-wide homologous recombination events and (2) crossing over on chromosome IV in mutants defective in RNaseH1, RNaseH2, or RNaseH1 and RNaseH2. Using a mutant DNA polymerase that incorporates 4-fold fewer rNMPs than wild type, I demonstrate that the primary recombinogenic lesion in the RNaseH2-defective genome is not rNMPs, but rather R-loops. This work suggests different in-vivo roles for RNaseH1 and RNaseH2 in resolving R-loops in yeast and is consistent with R-loops, not rNMPs, being the the likely source of pathology in Aicardi-Goutières Syndrome patients defective in RNaseH2.

Physical and Genetic Analysis of the CUP1 Tandem Array in the Yeast Saccharomyces cerevisiae

The genomes of many strains of baker’s yeast, Saccharomyces cerevisiae, contain multiple repeats of the copper-binding protein Cup1. Cup1 is a member of the metallothionein family, and is found in a tandem array on chromosome VIII. In this thesis, I describe studies that characterized these tandem arrays and their mechanism of formation across diverse strains of yeast. I show that CUP1 arrays are an illuminating model system for observing recombination in eukaryotes, and describe insights derived from these observations.

In our first study, we analyzed 101 natural isolates of S. cerevisiae in order to examine the diversity of CUP1-containing repeats across different strains. We identified five distinct classes of repeats that contain CUP1. We also showed that some strains have only a single copy of CUP1. By comparing the sequences of all the strains, we were able to elucidate the mechanism of formation of the CUP1 tandem arrays, which involved unequal non-homologous recombination events starting from a strain that had only a single CUP1 gene. Our observation of CUP1 repeat formation allows more general insights about the formation of tandem repeats from single-copy genes in eukaryotes, which is one of the most important mechanisms by which organisms evolve.

In our second study, we delved deeper into our mechanistic investigations by measuring the relative rates of inter-homolog and intra-/inter-sister chromatid recombination in CUP1 tandem arrays. We used a diploid strain that is heterozygous both for insertion of a selectable marker (URA3) inside the tandem array, and also for markers at either end of the array. The intra-/inter-sister chromatid recombination rate turned out to be more than ten-fold greater than the inter-homolog rate. Moreover, we found that loss of the proteins Rad51 and Rad52, which are required for most inter-homolog recombination, did not greatly reduce recombination in the CUP1 tandem repeats. Additionally, we investigated the effects of elevated copper levels on the rate of each type of recombination at the CUP1 locus. Both types of recombination are increased at high concentrations of copper (as is known to be the case for CUP1 transcription). Furthermore, the inter-homolog recombination rate at the CUP1 locus is higher than the average over the genome during mitosis, but is lower than the average during meiosis.

The research described in Chapter 2 is published in 2014.

Recent Reticulate Evolution in the Ecologically Dominant Lineage of Coccolithophores

The coccolithophore family Noëlaerhabdaceae contains a number of taxa that are very abundant in modern oceans, including the cosmopolitan bloom-forming Emiliania huxleyi. Introgressive hybridization has been suggested to account for incongruences between nuclear, mitochondrial and plastidial phylogenies of morphospecies within this lineage, but the number of species cultured to date remains rather limited. Here, we present the characterization of 5 new Noëlaerhabdaceae culture strains isolated from samples collected in the south-east Pacific Ocean. These were analyzed morphologically using scanning electron microscopy and phylogenetically by sequencing 5 marker genes (nuclear 18S and 28S rDNA, plastidial tufA, and mitochondrial cox1 and cox3 genes). Morphologically, one of these strains corresponded to Gephyrocapsa ericsonii and the four others to Reticulofenestra parvula. Ribosomal gene sequences were near identical between these new strains, but divergent from G. oceanica, G. muellerae, and E. huxleyi. In contrast to the clear distinction in ribosomal phylogenies, sequences from other genomic compartments clustered with those of E. huxleyi strains with which they share an ecological range (i.e., warm temperate to tropical waters). These data provide strong support for the hypothesis of past (and potentially ongoing) introgressive hybridization within this ecologically important lineage and for the transfer of R. parvula to Gephyrocapsa. These results have important implications for understanding the role of hybridization in speciation in vast ocean meta-populations of phytoplankton.

Recent Reticulate Evolution in the Ecologically Dominant Lineage of Coccolithophores

The coccolithophore family Noëlaerhabdaceae contains a number of taxa that are very abundant in modern oceans, including the cosmopolitan bloom-forming Emiliania huxleyi. Introgressive hybridization has been suggested to account for incongruences between nuclear, mitochondrial and plastidial phylogenies of morphospecies within this lineage, but the number of species cultured to date remains rather limited. Here, we present the characterization of 5 new Noëlaerhabdaceae culture strains isolated from samples collected in the south-east Pacific Ocean. These were analyzed morphologically using scanning electron microscopy and phylogenetically by sequencing 5 marker genes (nuclear 18S and 28S rDNA, plastidial tufA, and mitochondrial cox1 and cox3 genes). Morphologically, one of these strains corresponded to Gephyrocapsa ericsonii and the four others to Reticulofenestra parvula. Ribosomal gene sequences were near identical between these new strains, but divergent from G. oceanica, G. muellerae, and E. huxleyi. In contrast to the clear distinction in ribosomal phylogenies, sequences from other genomic compartments clustered with those of E. huxleyi strains with which they share an ecological range (i.e., warm temperate to tropical waters). These data provide strong support for the hypothesis of past (and potentially ongoing) introgressive hybridization within this ecologically important lineage and for the transfer of R. parvula to Gephyrocapsa. These results have important implications for understanding the role of hybridization in speciation in vast ocean meta-populations of phytoplankton.

AnnoTALE: Bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences

Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present 'AnnoTALE', a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities. © 2016, Nature Publishing Group. All rights reserved.

Impacto del Programa de Alimentación Escolar en el Trabajo Infantil: Una aproximación desde la toma de decisiones familiares

Esta investigación analiza el impacto del Programa de Alimentación Escolar en el trabajo infantil en Colombia a través de varias técnicas de evaluación de impacto que incluyen emparejamiento simple, emparejamiento genético y emparejamiento con reducción de sesgo. En particular, se encuentra que este programa disminuye la probabilidad de que los escolares trabajen alrededor de un 4%. Además, se explora que el trabajo infantil se reduce gracias a que el programa aumenta la seguridad alimentaria, lo que consecuentemente cambia las decisiones de los hogares y anula la carga laboral en los infantes. Son numerosos los avances en primera infancia llevados a cabo por el Estado, sin embargo, estos resultados sirven de base para construir un marco conceptual en el que se deben rescatar y promover las políticas públicas alimentarias en toda la edad escolar.

Desenlaces de la escala Omaha+ en los pacientes en cuidado intensivo en la fundación santa fe de Bogotá

Introducción La ventilación mecánica es fundamental en el manejo de la falla respiratoria aguda, actualmente no existe consenso sobre el momento exacto de extubación. Este estudio describe el comportamiento de la escala OMAHA+ en nuestra institución. Objetivo Principal Describir los desenlaces clínicos relacionados con la escala OMAHA+ durante la extubación de los pacientes de las unidades de cuidado intensivo del hospital universitario. Métodos Estudio descriptivo, retrospectivo, basado en el registro de la escala OMAHA+ de 68 pacientes durante el proceso de extubación en las Unidades de cuidado intensivo adulto de la Fundación Santa Fe de Bogotá durante Agosto de 2014 a Mayo de 2015. Resultados Se encontraron valores gasométricos cercanos a la normalidad, con una PaO2/FiO2 media de 261 (DS 60,6), SaO2 media de 96% (DS 2%), media de lactato sérico de 1.5 mmol/L (DS 1,2 mmol/L), con signos vitales normales. La causa más común de ingreso a UCI fue Neumonía, seguida por cirugía cardiaca y abdominal. Las medias de parámetros ventilatorios al momento de extubación fueron; PEEP de 6 (DS 0,8), volumen corriente de 8ml/Kg (DS 1,4 ml/Kg), índice de Tobín de 34 (DS 11,9), test de fuga positivo 94%, y sólo una extubación fallida. Conclusiones La escala OMAHA+ puede ser una herramienta útil, aplicable y fácilmente reproducible en los pacientes con soporte ventilatorio mecánico invasivo previo al proceso de extubación, con baja proporción de fallo. Estos resultados deben ser evaluados en estudios prospectivos.

Discovering Hands - México

El modelo de Discovering Hands ha sido reconocido internacionalmente como un proyecto innovador que se ha expandido por diferentes países del mundo, como Austria, y se ha empezado a estudiar la propuesta en países como República Checa, India y Colombia. (Discovering Hands, 2016). Esto se debe a que no solo mejora el tratamiento de cáncer de mama, sino que también reduce los costos totales de tratamiento de la enfermedad y aumenta la fuerza laborar de los países donde esté presente. Al representar una gran oportunidad en diferentes aspectos, se quiso desarrollar un estudio de factibilidad del modelo de negocio en tres países de América Latina, Colombia –donde ya se encuentra en marcha un proyecto piloto liderado por la CAF en Cali - , Argentina y México. El presente trabajo consiste en dicho estudio de factibilidad, focalizado en México; por medio de este se buscaron tres cosas primordiales, conocer y estudiar el contexto del mercado y situación de salud en el país, analizar los datos recogidos, con el fin de proponer soluciones para disminuir una de las principales causas de muerte en el país. Actualmente en México el 52% de casos de cáncer de mama diagnosticados sucede en etapas tard��as, aumentando el riesgo de muerte de los pacientes (Colima, 2013). Con el estudio se logró identificar una oportunidad potencial para Discovering Hands siendo su estrategia un recurso adicional para contribuir a mejorar el diagnóstico precoz de cáncer de mama en el país y debido a esto se presenta un modelo de negocio adaptable a las necesidades mexicanas

Das Grosse Zumahlen Geistliche Elend Des Jüdischen Volckes Bey Gelegenheit Einer Juden-Tauffe : Aus 2. Cor. III, 15.16.17 In der Hospital-Kirche d. 29. Aug. 1743 Der Zahlreichen Gemeinde des Herrn vorgetragen, Und heraus gegeben Von Gottfried Thomas Zeitmann, Evangel. Prediger in Franckfurt am Mayn

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Paradise Regain'd : a poem, in four books ; To which is added Samson agonistes and Poems upon several Occasions / by Thomas Newton ; volume the second.

Mode of access: Internet.

The life of Thomas Jefferson, esq., LL. D., late ex president of the United States:

Portrait engraved by Neagle.