Altos fluxos positivos de metano para a atmosfera foram detectados na região amazônica. O gás metano é o segundo mais importante gás de efeito estufa e micro-organismos pertencentes ao Domínio Archaea são responsáveis pela produção de aproximadamente 70% do metano emitido para a atmosfera anualmente. O objetivo deste trabalho foi caracterizar a diversidade de arqueias em sedimentos dos rios Floresta e Madeira através de técnicas moleculares e do cultivo de arqueias metanogênicas. A maior parte das sequências obtidas nas duas bibliotecas pertence ao domínio Crenarchaeota, algumas com similaridade menor que 97% às sequências depositadas nos bancos de dados, revelando a existência de grupos ainda não descritos na literatura. Nos enriquecimentos do sedimento do rio Madeira detectaram-se células pertencentes às famílias Methanosarcinaceae e Methanobacteriaceae pelo emprego de sondas fluorescentes de RNA. Culturas dos gêneros Methanosarcina e Methanobacterium foram estabelecidas em laboratório. A grande diversidade de arqueias não cultivadas encontrada vem reforçar a necessidade de se estudar esse grupo, especialmente sua fisiologia e, consequentemente, seu papel ecológico nos diversos ambientes em que são encontrados. / High positive fluxes of methane to the atmosphere have been detected in the Amazonian region. Methane is the second most important greenhouse gas and microorganisms belonging to the Archaea domain are responsible for approximately 70% of the total methane emitted to the atmosphere annually. The objective of this work was to characterize the Archaea diversity in two sites at Madeira and Floresta rivers sediments using molecular techniques and the culturing of methanogenic archaea. Most sequences obtained in the libraries from both rivers belonged to the Crenarchaeota domain, and around half of them presented less than 97% of similarity to sequences available in databases, revealing the existence of new archaea groups yet to be described in the literature. Cells belonging to the Methanosarcinaceae and Methanobacteriaceae families were detected in the enrichment cultures from Madeira River through the use of RNA fluorescent probes. Strains of Methanosarcina sp. and Methanobacterium sp. are being maintained under laboratory conditions. The great diversity of uncultured Archaea found emphasizes the need to study this group, mainly its physiology and, consequently, its role in the diverse environments they occupy.

Thesis (Ph.D. in Biophysics & Genetics, Program in Molecular Biology) -- University of Colorado Denver, 2007. / Typescript. Includes bibliographical references (leaves 90-98). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;

Altos fluxos positivos de metano para a atmosfera foram detectados na região amazônica. O gás metano é o segundo mais importante gás de efeito estufa e micro-organismos pertencentes ao Domínio Archaea são responsáveis pela produção de aproximadamente 70% do metano emitido para a atmosfera anualmente. O objetivo deste trabalho foi caracterizar a diversidade de arqueias em sedimentos dos rios Floresta e Madeira através de técnicas moleculares e do cultivo de arqueias metanogênicas. A maior parte das sequências obtidas nas duas bibliotecas pertence ao domínio Crenarchaeota, algumas com similaridade menor que 97% às sequências depositadas nos bancos de dados, revelando a existência de grupos ainda não descritos na literatura. Nos enriquecimentos do sedimento do rio Madeira detectaram-se células pertencentes às famílias Methanosarcinaceae e Methanobacteriaceae pelo emprego de sondas fluorescentes de RNA. Culturas dos gêneros Methanosarcina e Methanobacterium foram estabelecidas em laboratório. A grande diversidade de arqueias não cultivadas encontrada vem reforçar a necessidade de se estudar esse grupo, especialmente sua fisiologia e, consequentemente, seu papel ecológico nos diversos ambientes em que são encontrados. / High positive fluxes of methane to the atmosphere have been detected in the Amazonian region. Methane is the second most important greenhouse gas and microorganisms belonging to the Archaea domain are responsible for approximately 70% of the total methane emitted to the atmosphere annually. The objective of this work was to characterize the Archaea diversity in two sites at Madeira and Floresta rivers sediments using molecular techniques and the culturing of methanogenic archaea. Most sequences obtained in the libraries from both rivers belonged to the Crenarchaeota domain, and around half of them presented less than 97% of similarity to sequences available in databases, revealing the existence of new archaea groups yet to be described in the literature. Cells belonging to the Methanosarcinaceae and Methanobacteriaceae families were detected in the enrichment cultures from Madeira River through the use of RNA fluorescent probes. Strains of Methanosarcina sp. and Methanobacterium sp. are being maintained under laboratory conditions. The great diversity of uncultured Archaea found emphasizes the need to study this group, mainly its physiology and, consequently, its role in the diverse environments they occupy.

Indiana University-Purdue University Indianapolis (IUPUI) / Toxoplasma gondii, a single-celled eukaryotic pathogen, has infected one-third of the world’s population and is the causative agent of toxoplasmosis. The disease primarily affects immunocompromised individuals such as AIDS, cancer, and transplant patients. The parasites can infect any nucleated cell in warm-blooded vertebrates, but because they preferentially target CNS, heart, and ocular tissue, manifestations of infection often include encephalitis, myocarditis, and a host of neurological and ocular disorders. Toxoplasma can also be transmitted congenitally by a mother who becomes infected for the first time during pregnancy, which may result in spontaneous abortion or birth defects in the child. Unfortunately, the therapy currently available for treating toxoplasmosis exhibits serious side effects and can cause severe allergic reactions. Therefore, there is a desperate need to identify novel drug targets for developing more effective, less toxic treatments. The regulation of proteins via lysine acetylation, a reversible post-translational modification, has previously been validated as a promising avenue for drug development. Lysine acetyltransferases (KATs) are responsible for the acetylation of hundreds of proteins throughout prokaryotic and eukaryotic cells. In Toxoplasma, we identified a KAT that exhibits homology to Elongator protein 3 (TgElp3), the catalytic component of a transcriptional elongation complex. TgElp3 contains the highly conserved radical S-adenosylmethionine and KAT domains but also possesses a unique C-terminal transmembrane domain (TMD). Interestingly, we found that the TMD anchors TgElp3 in the outer mitochondrial membrane (OMM) such that the catalytic domains are oriented towards the cytosol. Our results uncovered the first tail-anchored mitochondrial KAT reported for any species to date. We also discovered a shortened form of Elp3 present in mouse mitochondria, suggesting that Elp3 functions beyond transcriptional elongation across eukaryotes. Furthermore, we established that TgElp3 is essential for parasite viability and that its OMM localization is important for its function, highlighting its value as a potential target for future drug development.

Indiana University-Purdue University Indianapolis (IUPUI) / In response to different environmental stresses, phosphorylation of eukaryotic initiation factor-2 (eIF2) rapidly reduces protein synthesis, which lowers energy expenditure and facilitates reprogramming of gene expression to remediate stress damage. Central to the changes in gene expression, eIF2 phosphorylation also enhances translation of ATF4, a transcriptional activator of genes subject to the Integrated Stress Response (ISR). The ISR increases the expression of genes important for alleviating stress, or alternatively triggering apoptosis. One ISR target gene encodes the transcriptional regulator CHOP whose accumulation is critical for stress-induced apoptosis. In this dissertation research, I show that eIF2 phosphorylation induces preferential translation of CHOP by a mechanism involving a single upstream ORF (uORF) located in the 5’-leader of the CHOP mRNA. In the absence of stress and low eIF2 phosphorylation, translation of the uORF serves as a barrier that prevents translation of the downstream CHOP coding region. Enhanced eIF2 phosphorylation during stress facilitates ribosome bypass of the uORF, and instead results in the translation of CHOP. Stable cell lines were also constructed that express CHOP transcript containing the wild type uORF or deleted for the uORF and each were analyzed for expression changes in response to the different stress conditions. Increased CHOP levels due to the absence of inhibitory uORF sensitized the cells to stress-induced apoptosis when compared to the cells that express CHOP mRNA containing the wild type uORF. This new mechanism of translational control explains how expression of CHOP and the fate of cells are tightly linked to the levels of phosphorylated eIF2 and stress damage.

Indiana University-Purdue University Indianapolis (IUPUI) / In response to different environmental stresses, phosphorylation of eIF2 (eIF2P) represses global translation coincident with preferential translation of ATF4. ATF4 is a transcriptional activator of the integrated stress response, a program of gene expression involved in metabolism, nutrient uptake, anti-oxidation, and the activation of additional transcription factors, such as CHOP/GADD153, that can induce apoptosis. Although eIF2P elicits translational control in response to many different stress arrangements, there are selected stresses, such as exposure to UV irradiation, that do not increase ATF4 expression despite robust eIF2P. In this study we addressed the underlying mechanism for variable expression of ATF4 in response to eIF2P during different stress conditions and the biological significance of omission of enhanced ATF4 function. We show that in addition to translational control, ATF4 expression is subject to transcriptional regulation. Stress conditions such as endoplasmic reticulum stress induce both transcription and translation of ATF4, which together enhance expression of ATF4 and its target genes in response to eIF2P. By contrast, UV irradiation represses ATF4 transcription, which diminishes ATF4 mRNA available for translation during eIF2∼P. eIF2P enhances cell survival in response to UV irradiation. However, forced expression of ATF4 and its target gene CHOP leads to increased sensitivity to UV irradiation. In this study, we also show that C/EBPβ is a transcriptional repressor of ATF4 during UV stress. C/EBPβ binds to critical elements in the ATF4 promoter resulting in its transcriptional repression. The LIP isoform of C/EBPβ, but not the LAP version is regulated following UV exposure and directly represses ATF4 transcription. Loss of the LIP isoform results in increased ATF4 mRNA levels in response to UV irradiation, and subsequent recovery of ATF4 translation, leading to enhanced expression of its target genes. Together these results illustrate how eIF2P and translational control, combined with transcription factors regulated by alternative signaling pathways, can direct programs of gene expression that are specifically tailored to each environmental stress.

L'incessant augment del nombre de seqüències genòmiques, juntament amb l'increment del nombre de tècniques experimentals de les que es disposa, permetrà obtenir el catàleg complet de les funcions cel.lulars de diferents organismes, incloent-hi la nostra espècie. Aquest catàleg definirà els fonaments sobre els que es podrà entendre millor com els organismes funcionen a nivell molecular. Al mateix temps es tindran més pistes sobre els canvis que estan associats amb les malalties. Per tant, la seqüència en brut, tal i com s'obté dels projectes de seqüenciació de genomes, no té cap valor sense les anàlisis i la subsegüent anotació de les característiques que defineixen aquestes funcions. Aquesta tesi presenta la nostra contribució en tres aspectes relacionats de l'anotació dels gens en genomes eucariotes. Primer, la comparació a nivell de seqüència entre els genomes humà i de ratolí es va dur a terme mitjançant un protocol semi-automàtic. El programa de predicció de gens SGP2 es va desenvolupar a partir d'elements d'aquest protocol. El concepte al darrera de l'SGP2 és que les regions de similaritat obtingudes amb el programa TBLASTX, es fan servir per augmentar la puntuació dels exons predits pel programa geneid, amb el que s obtenen conjunts d'anotacions més acurats d'estructures gèniques. SGP2 té una especificitat que és prou gran com per que es puguin validar experimentalment via RT-PCR. La validació de llocs d'splicing emprant la tècnica de la RT-PCR és un bon exemple de com la combinació d'aproximacions computacionals i experimentals produeix millors resultats que per separat. S'ha dut a terme l'anàlisi descriptiva a nivell de seqüència dels llocs d'splicing obtinguts sobre un conjunt fiable de gens ortòlegs per humà, ratolí, rata i pollastre. S'han explorat les diferències a nivell de nucleòtid entre llocs U2 i U12, pel conjunt d'introns ortòlegs que se'n deriva d'aquests gens. S'ha trobat que els senyals d'splicing ortòlegs entre humà i rossegadors, així com entre rossegadors, estan més conservats que els llocs no relacionats. Aquesta conservació addicional pot ser explicada però a nivell de conservació basal dels introns. D'altra banda, s'ha detectat més conservació de l'esperada entre llocs d'splicing ortòlegs entre mamífers i pollastre. Els resultats obtinguts també indiquen que les classes intròniques U2 i U12 han evolucionat independentment des de l'ancestre comú dels mamífers i les aus. Tampoc s'ha trobat cap cas convincent d'interconversió entre aquestes dues classes en el conjunt d'introns ortòlegs generat, ni cap cas de substitució entre els subtipus AT-AC i GT-AG d'introns U12. Al contrari, el pas de GT-AG a GC-AG, i viceversa, en introns U2 no sembla ser inusual. Finalment, s'han implementat una sèrie d'eines de visualització per integrar anotacions obtingudes pels programes de predicció de gens i per les anàlisis comparatives sobre genomes. Una d'aquestes eines, el gff2ps, s'ha emprat en la cartografia dels genomes humà, de la mosca del vinagre i del mosquit de la malària, entre d'altres. El programa gff2aplot i els filtres associats, han facilitat la tasca d'integrar anotacions de seqüència amb els resultats d'eines per la cerca d'homologia, com ara el BLAST. S'ha adaptat també el concepte de pictograma a l'anàlisi comparativa de llocs d splicing ortòlegs, amb el desenvolupament del programa compi. / El aumento incesante del número de secuencias genómicas, junto con el incremento del número de técnicas experimentales de las que se dispone, permitirá la obtención del catálogo completo de las funciones celulares de los diferentes organismos, incluida nuestra especie. Este catálogo definirá las bases sobre las que se pueda entender mejor el funcionamiento de los organismos a nivel molecular. Al mismo tiempo, se obtendrán más pistas sobre los cambios asociados a enfermedades. Por tanto, la secuencia en bruto, tal y como se obtiene en los proyectos de secuenciación masiva, no tiene ningún valor sin los análisis y la posterior anotación de las características que definen estas funciones. Esta tesis presenta nuestra contribución a tres aspectos relacionados de la anotación de los genes en genomas eucariotas. Primero, la comparación a nivel de secuencia entre el genoma humano y el de ratón se llevó a cabo mediante un protocolo semi-automático. El programa de predicción de genes SGP2 se desarrolló a partir de elementos de dicho protocolo. El concepto sobre el que se fundamenta el SGP2 es que las regiones de similaridad obtenidas con el programa TBLASTX, se utilizan para aumentar la puntuación de los exones predichos por el programa geneid, con lo que se obtienen conjuntos más precisos de anotaciones de estructuras génicas. SGP2 tiene una especificidad suficiente como para validar esas anotaciones experimentalmente vía RT-PCR. La validación de los sitios de splicing mediante el uso de la técnica de la RT-PCR es un buen ejemplo de cómo la combinación de aproximaciones computacionales y experimentales produce mejores resultados que por separado. Se ha llevado a cabo el análisis descriptivo a nivel de secuencia de los sitios de splicing obtenidos sobre un conjunto fiable de genes ortólogos para humano, ratón, rata y pollo. Se han explorado las diferencias a nivel de nucleótido entre sitios U2 y U12 para el conjunto de intrones ortólogos derivado de esos genes. Se ha visto que las señales de splicing ortólogas entre humanos y roedores, así como entre roedores, están más conservadas que las no ortólogas. Esta conservación puede ser explicada en parte a nivel de conservación basal de los intrones. Por otro lado, se ha detectado mayor conservación de la esperada entre sitios de splicing ortólogos entre mamíferos y pollo. Los resultados obtenidos indican también que las clases intrónicas U2 y U12 han evolucionado independientemente desde el ancestro común de mamíferos y aves. Tampoco se ha hallado ningún caso convincente de interconversión entre estas dos clases en el conjunto de intrones ortólogos generado, ni ningún caso de substitución entre los subtipos AT-AC y GT-AG en intrones U12. Por el contrario, el paso de GT-AG a GC-AG, y viceversa, en intrones U2 no parece ser inusual. Finalmente, se han implementado una serie de herramientas de visualización para integrar anotaciones obtenidas por los programas de predicción de genes y por los análisis comparativos sobre genomas. Una de estas herramientas, gff2ps, se ha utilizado para cartografiar los genomas humano, de la mosca del vinagre y del mosquito de la malaria. El programa gff2aplot y los filtros asociados, han facilitado la tarea de integrar anotaciones a nivel de secuencia con los resultados obtenidos por herramientas de búsqueda de homología, como BLAST. Se ha adaptado también el concepto de pictograma al análisis comparativo de los sitios de splicing ortólogos, con el desarrollo del programa compi. / The constantly increasing amount of available genome sequences, along with an increasing number of experimental techniques, will help to produce the complete catalog of cellular functions for different organisms, including humans. Such a catalog will define the base from which we will better understand how organisms work at the molecular level. At the same time it will shed light on which changes are associated with disease. Therefore, the raw sequence from genome sequencing projects is worthless without the complete analysis and further annotation of the genomic features that define those functions. This dissertation presents our contribution to three related aspects of gene annotation on eukaryotic genomes. First, a comparison at sequence level of human and mouse genomes was performed by developing a semi-automatic analysis pipeline. The SGP2 gene-finding tool was developed from procedures used in this pipeline. The concept behind SGP2 is that similarity regions obtained by TBLASTX are used to increase the score of exons predicted by geneid, in order to produce a more accurate set of gene structures. SGP2 provides a specificity that is high enough for its predictions to be experimentally verified by RT-PCR. The RT-PCR validation of predicted splice junctions also serves as example of how combined computational and experimental approaches will yield the best results. Then, we performed a descriptive analysis at sequence level of the splice site signals from a reliable set of orthologous genes for human, mouse, rat and chicken. We have explored the differences at nucleotide sequence level between U2 and U12 for the set of orthologous introns derived from those genes. We found that orthologous splice signals between human and rodents and within rodents are more conserved than unrelated splice sites. However, additional conservation can be explained mostly by background intron conservation. Additional conservation over background is detectable in orthologous mammalian and chicken splice sites. Our results also indicate that the U2 and U12 intron classes have evolved independently since the split of mammals and birds. We found neither convincing case of interconversion between these two classes in our sets of orthologous introns, nor any single case of switching between AT-AC and GT-AG subtypes within U12 introns. In contrast, switching between GT-AG and GC-AG U2 subtypes does not appear to be unusual. Finally, we implemented visualization tools to integrate annotation features for gene- finding and comparative analyses. One of those tools, gff2ps, was used to draw the whole genome maps for human, fruitfly and mosquito. gff2aplot and the accompanying parsers facilitate the task of integrating sequence annotations with the output of homologybased tools, like BLAST.We have also adapted the concept of pictograms to the comparative analysis of orthologous splice sites, by developing compi.

Derived from and inspired by the adaptive immune system of bacteria, CRISPR has gone from basic biology knowledge to a revolutionizing biotechnological tool, applicable in many research areas such as medicine, industry and agriculture. The full mechanism of CRISPR-Cas9 was first published in 2012 and various CRISPR-Cas systems have already passed the first stages of clinical trials as new gene therapies. The immense research has resulted in continuously growing knowledge of CRISPR systems and the technique seems to have the potential to greatly impact all life on our planet. Therefore, this literature study aims to thoroughly describe the CRISPR-Cas system, and further suggest an undergraduate laboratory exercise involving gene editing with the CRISPR-Cas9 tool. In this paper, we describe the fundamental technical background of the CRISPR-Cas system, especially emphasizing the most studied CRISPR-Cas9 system, its development and applications areas, as well as highlighting its current limitations and ethical concerns. The history of genetic engineering and the discovery of the CRISPR system is also described, along with a comparison with other established gene editing techniques.  This study concludes that a deeper knowledge about CRISPR is important and required since the technique is applicable in many research areas. A laboratory exercise will not only inspire but also provide extended theoretical and practical knowledge for undergraduate students.

Indiana University-Purdue University Indianapolis (IUPUI) / An excess of bone resorption over bone formation leads to osteoporosis, resulting in a reduction of bone mass and an increase in the risk of bone fracture. Anabolic and anti-resorptive drugs are currently available for treatment, however, none of these drugs are able to both promote osteoblastogenesis and reduce osteoclastogenesis. This thesis focused on the role of eukaryotic translation initiation factor 2 alpha (eIF2alpha), which regulates efficiency of translational initiation. The elevation of phosphorylated eIF2alpha was reported to stimulate osteoblastogenesis, but its effects on osteoclastogenesis have not been well understood. Using synthetic chemical agents such as salubrinal and guanabenz that are known to inhibit the de-phosphorylation of eIF2alpha, the role of phosphorylation of eIF2alpha in osteoclastogenesis was investigated in this thesis. The questions addressed herein were: Does the elevation of phosphorylated eIF2alpha (p-eIF2alpha) by salubrinal and guanabenz alter osteoclastogenesis? If so, what regulatory mechanism mediates the process? It was hypothesized that p-eIF2alpha could attenuate the development of osteoclast by regulating the transcription factor(s) amd microRNA(s) involved in osteoclastogenesis. To test this hypothesis, we conducted in vitro and in silico analysis of the responses of RAW 264.7 pre-osteoclast cells to salubrinal and guanabenz. First, the in vitro results revealed that the elevated level of phosphorylated eIF2alpha inhibited the proliferation, differentiation, and maturation of RAW264.7 cells and downregulated the expression of NFATc1, a master transcription factor of osteoclastogenesis. Silencing eIF2alpha by RNA interference suppressed the downregulation of NFATc1, suggesting the involvement of eIF2alpha in regulation of NFATc1. Second, the in silico results using genome-wide expression data and custom-made Matlab programs predicted a set of stimulatory and inhibitory regulator genes as well as microRNAs, which were potentially involved in the regulation of NFATc1. RNA interference experiments indicated that the genes such as Zfyve21 and Ddit4 were primary candidates as an inhibitor of NFATc1. In summary, the results showed that the elevation of p-eIF2alpha by salubrinal and guanabenz leads to attenuation of osteoclastogenesis through the downregulation of NFATc1. The regulatory mechanism is mediated by eIF2alpha signaling, but other signaling pathways are likely to be involved. Together with the previous data showing the stimulatory role of p-eIF2alpha in osteoblastogenesis, the results herein suggest that eIF2alpha-mediated signaling could provide a novel therapeutic target for treatment of osteoporosis by promoting bone formation and reducing bone resorption.

Indiana University-Purdue University Indianapolis (IUPUI) / Translation Initiation in protein synthesis is a crucial step controlling gene expression that enhanced by eukaryotic translation initiation factors (eIFs). eIF3a, the largest subunit of eIF3 complexes, has been shown to regulate protein synthesis and cellular response to cisplatin treatment. Its expression has also been shown to negatively associate with prognosis. In this study, we tested a hypothesis that eIF3a regulates synthesis of proteins important for repair of double strand DNA breaks induced by ionizing radiation (IR). We found that eIF3a up-regulation sensitizes cellular response to IR while its knockdown causes resistance to IR. We also found that eIF3a over-expression increases IR-induced DNA damage and decreases Non-Homologous End Joining (NHEJ) activity by suppressing expression level of NHEJ repair proteins such as DNA-PKcs and vice versa. Together, we conclude that eIF3a plays an important role in cellular response to DNA-damaging treatments by regulating synthesis of DNA repair proteins and, thus, eIIF3a likely plays an important role in the outcome of cancer patients treated with DNA-damaging strategies including ionizing radiation.