Thesis (Ph. D.)--West Virginia University, 2006. / Title from document title page. Document formatted into pages; contains vi, 143 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 115-127).

Made available in DSpace on 2014-06-11T19:27:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-08-20Bitstream added on 2014-06-13T19:55:44Z : No. of bitstreams: 1 sobrinho_lsv_me_araca.pdf: 921356 bytes, checksum: 29d3e58899a35e5de14b32e263c2fe77 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O objetivo do presente estudo foi determinar em uma população de 302 gatos provenientes de área endêmica para leishmaniose visceral, a prevalência da infecção por Leishmania spp. e a presença de coinfecção pelo Toxoplasma gondii, vírus da imunodeficiência felina (FIV) e vírus da leucemia felina (FeLV). Foram evidenciadas formas amastigotas de Leishmania spp. em 9,93% (30/302) dos animais. A prevalência da leishmaniose observada por meio dos métodos de ELISA-proteína A, ELISA-IgG ou exame parasitológico direto foi de 21,85% (66/302), sendo 13,64% (9/66) positivos no exame parasitológico direto e sororeagentes nas técnicas de ELISA indireto. Doze animais (70,59%) foram sororeagentes para o FIV e a Leishmania spp., enquanto 17 (25,76%) apresentaram anticorpos anti-Toxoplasma gondii e anti-Leishmania spp. e cinco (71,43%) apresentavam infecção pelos três agentes. Não foi observada coinfecção entre Leishmania spp. e o FeLV. Houve associação estatisticamente significante entre a coinfecção por Leishmania spp. e pelo vírus da imunodeficiência felina, bem como entre a presença de Leishmania spp., do vírus da imunodeficiência felina e do Toxoplasma gondii. A sensibilidade e a especificidade dos métodos de ELISA-proteína A, ELISA-IgG e reação de imunofluorescência indireta para o diagnóstico de leishmaniose felina foram de 56,6% e 89,47%, 55,55% e 90,96% e 54,55% e 96,80%, respectivamente. As concordâncias entre a RIFI e as técnicas de ELISA-proteína A e ELISA-IgG foram fracas. No entanto, houve boa concordância entre as duas últimas técnicas. O presente estudo verificou que gatos residentes em área endêmica para leishmaniose visceral são predispostos à coinfecção por Leishmania spp. e vírus da imunodeficiência felina, e que parte deles desenvolvem sintomas inespecíficos e devem ser investigados em um diagnóstico diferencial / The aim of this study was to determine, in a population of 302 cats from an endemic area for visceral leishmaniasis, the prevalence of the infection by Leishmania spp. and the presence of co-infection by Toxoplasma gondii, feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV). Amastigote forms of Leishmania spp were evidenced in 9.93% (30/302) of the animals. Prevalence of leishmaniasis by ELISA-prot A, ELISA-IgG or direct parasitological examination was 21.85% (66/302), being 13.64% (9/66) positive in both direct parasitological examination and ELISA. Twelve animals (70.59%) were seroreagent for FIV and Leishmania spp., while 17 (25.76%) showed antibodies against Toxoplasma gondii and Leishmania spp. and five (71.43%) showed antibodies against those three agents. Co-infection was not observed between Leishmania spp. and FeLV. There was statistically significant correlation between the co-infection by Leishmania spp. and by the immunodeficiency virus, as well as among the present of Leishmania spp, feline immunodeficiency virus and Toxoplasma gondii. The susceptibility and the specificities of (the methods) ELISA-prot A, ELISA-IgG and reaction of indirect immunofluorescence for the diagnosis of feline leishmaniasis were 56.6% and 89.47%, 55.55% and 90.96% and 54.55% and 96.80%, respectively. The agreements between RIFI and ELISA-prot A and ELISA-IgG techniques were weak. However, there was a good agreement between the last two techniques. This study verified that cats from endemic areas for visceral leishmaniasis are predisposed to co-infection by Leishmania spp. and feline immunodeficiency virus, and that part of them developed nonspecific symptoms and should be investigated in a differential diagnosis

Breast cancer is the most common cancer in women and research efforts to unravel the underlying mechanisms that drive carcinogenesis are continuous. The emergence of high-throughput sequencing techniques and their constant advancement, in combination with large scale studies of genomic and transcriptomic data, allowed the identification of important genetic changes that take place in the breast cancer genome, including somatic mutations, copy number aberrations and genomic rearrangements.The overall aim of this thesis is to explore the presence of genetic changes that take place in the breast cancer transcriptome and their possible contribution to carcinogenesis. The aim of the first research study was the identification of expressed gene fusions in breast cancer and the study of their association with other genomic events. For achieving this, transcriptome sequencing and Single Nucleotide Polymorphism arrays data for a cohort of 55 tumors and 10 normal breast tissues were combined. Gene fusions were detected in the majority of the samples, with evident differences between breast cancer subtypes, where HER2+ samples had significantly more fusions than the other subtypes. The genome-wide analysis uncovered localization of fusion genes in specific chromosomes like 17, 8 or 20. Additionally, a positive correlation between the number of gene fusions and the number of amplifications was observed, including the association between fusions on chromosome 17 and the amplifications in HER2+ samples, which can be attributed to the highly rearranged genomes of these subtypes. Finally, the absence of highly recurrent fusions across this cohort adds to the notion that gene fusions in breast cancer are most likely private events, with the majority being “passenger” events. In the second research study, the aim was to identify a connection between viral infections and breast cancer by devising five different computational methods for the analysis of both transcriptome and exome data in a cohort of 58 breast tumors. Despite being able to detect viral sequences in our testing dataset, no significantly high numbers of viral sequences were detected in our samples. Specifically, viral sequences (~2-30 reads) were extracted belonging to viruses EBV, HHV6 and Merkel cell polyomavirus. Such low levels of viral expression direct against a viral etiology for breast cancer but one should not exclude possible cases of integrated but silent viruses.In the third research project, we analyzed in silico the transcriptional profiles of human endogenous retroviruses in breast cancer. Despite being scattered across the genome in large numbers, a number of ERVs are actively transcribed, consisting of a small percentage of the total mapped reads. Alongside protein coding genes and lncRNAs, they show distinct expression profiles across the different breast cancer subtypes with luminal and basal-like samples clear separating from each other. Additionally, distinct profiles between ER+ and ER- samples were observed. Tumor specific ERV loci show an association with the immune status of the tumors, indicating that ERVs are reactivated in tumors and could play a role in the activation of the immune response cascade.The results presented in this thesis exhibit only in a small fragment the diversity and heterogeneity of the breast cancer transcriptome. The strength of the sequencing techniques allows the in depth detection of different genomic events. Gene fusions should be considered as part of the breast cancer transcriptome but their low recurrence across samples indicates for a role as passenger events. Under the light of existing results, viral infections do not play a significant role in breast cancer. On the other hand, human endogenous retroviruses, despite originating from exogenous viruses, seems to exhibit transcriptional profiles similar to those of normal genes, indicating that they are part of the genome’s transcriptional machinery. / Doctorat en Sciences biomédicales et pharmaceutiques (Médecine) / info:eu-repo/semantics/nonPublished

Les cellules eucaryotes ont évolué de façon à s'assurer qu'aucun ARNm contenant des introns ne soit exporté du noyau. Néanmoins, les rétrovirus ont besoin d'exporter leur ARN non-épissé vers le cytoplasme afin de servir de matrice pour la traduction des protéines virales, ou d'être encapsidé comme ARN génomique dans les néo-virions. Différentes stratégies ont alors été mises en place par ces virus dans le but de détourner les voies d'export nucléaire cellulaires pour mener à bien l'export de leur ARN non-épissé. Le virus de la leucémie murine (MLV), l'un des premier rétrovirus de mammifère découvert, possède un génome qui, à l'inverse d'autres rétrovirus ne permet pas de coder pour des protéines accessoires pouvant aider à l'export de son ARN non-épissé. Bien que différentes séquences cis-régulatrices présentes sur l'ARN non-épissé ont été montrées comme favorisant l'export nucléaire de cet ARN, la/(les) voie(s) d'export détournée(s) par le MLV reste(nt) jusqu'alors inconnue(s).Dans les travaux présentés ici nous démontrons que le virus du MLV est capable de détourner la voie d'export cellulaire Tap pour exporter ses ARN épissé et non-épissé du noyau. Cet export permet notamment au virus d'exprimer ses protéines structurales et enzymatiques. De plus, nos résultats suggèrent également que l'export de l'ARN non-épissé du MLV est aussi possible par la voie d'export cellulaire CRM1, afin de favoriser leur encapsidation. En résumé, nos données révèlent un mode de régulation complexe, mis en place par le MLV, afin d'exporter l'ARN non-épissé et ainsi de distinguer sa destinée. / Eukaryotic cells have evolved to ensure that intron-containing mRNA do not leave the nucleus. However, retroviruses must export their intron-containing RNA in the cytoplasm to be either translated in viral proteins or packaged as genomic RNA in progeny viruses. Then, retroviruses are using different mechanisms in order to hijack cellular nuclear export pathway to export their unspliced RNA. Murine leukemia virus (MLV) is a simple retrovirus, one of the first discovered, which do not have the possibility to encode accessory proteins to help its unspliced RNA export. Although several cis-elements of the MLV unspliced RNA have been identified to regulate the cytoplasmic accumulation of this RNA, the pathway(s) hijacked by the MLV is(are) unrevealed until today. The researches present in this manuscript show that the MLV is able to hijack the cellular export pathway Tap dependant to export its spiced and unspliced RNA from the nucleus. This export leads to the expression of structural and enzymatic viral proteins. Moreover, our results suggest that the MLV can also hijack the cellular export factor CRM1 to export its unspliced RNA in order to package them. Finally, our data reveal the existence of a complex regulation mechanism use by the MLV to export and distinguish unspliced RNA regarding their destiny.

Le genre des Deltaretrovirus est composé des virus de la leucose bovine (BLV) et des virus T-lymphotropes de primates (PTLV-1, -2, -3 et -4) qui regroupent les virus humains T-lymphotropes (HTLV-1, -2, -3 et -4) et les virus simiens apparentés (STLV-1, -2, -3 et -4). Seules les infections par les PTLV-1 et BLV sont associées à des pathologies : une lymphoprolifération maligne appelée ATLL chez l'homme et le singe ou une maladie neurologique appelée HAM/TSP chez l'homme infectés par les PTLV-1 et une lymphoproliferation maligne chez les bovins infectés par BLV. L'infection par HTLV-2 n'est associée qu'à une lymphocytose et le pouvoir pathogène d'HTLV-3 n'est pas caractérisé à ce jour. Les lentivirus, parmi lesquels on trouve les agents étiologiques du SIDA VIH-1 et VIH-2, et les Deltaretrovirus, sont des rétrovirus complexes. Ils codent donc, en plus des protéines structurales et enzymatiques, pour des protéines régulatrices ainsi que pour des protéines auxiliaires qui seront au centre des travaux présentés. Chez HTLV-1 et BLV, les protéines auxiliaires jouent un rôle primordial dans l'infectiosité in vivo. Or ces protéines n'avaient pas encore été décrites chez les PTLV-3. Leur caractérisation composait donc le premier objectif de ces travaux de thèse. Nous avons ainsi identifié les ARN messagers codant 3 nouvelles protéines putatives in vitro. Nous avons étudié les caractéristiques de ces protéines, notamment leur rôle dans le cycle des PTLV-3 in vitro et leur expression in vivo. Dans un second travail, nous avons essayé de comprendre si les différents domaines fonctionnels déjà identifiés dans la protéine Vpx, une protéine auxiliaire de VIH-2 influençaient sa capacité à interagir avec le facteur de restriction cellulaire SAMHD-1. Nous avons voulu déterminer le compartiment cellulaire dans lequel Vpx induisait la dégradation de SAMHD-1 et la cinétique de ce phénomène, qui permet à ce virus de se répliquer dans les lignées myéloïdes. Ces travaux apportent des éléments nouveaux dans la compréhension du rôle des protéines auxiliaires sur la régulation fine du cycle rétroviral et l'échappement au système immunitaire inné / Deltaretroviruses include bovine leukemia viruses (BLV) and primate Tlymphotropic viruses (PTLV-1, -2, -3 and -4) which are composed of human Tlymphotropic (HTLV-1, -2, -3 and -4) and of their simian counterparts (STLV-1, -2, -3 and -4). PTLV-1 and BLV are the only ones associated to pathologies: a lymphoproliferative disorder named ATLL in humans and non human primates and a neurological disorder named HAM/TSP in humans in the case of PTLV-1 and a Bmalignant lymphoproliferation in BLV infected cattle. HTLV-2 has not been associated with any disease so far and the pathogenic potential of HTLV-3 remains unknown. Lentiviruses, including HIV-1 and -2 the AIDS etiological agents, and Deltaretroviruses, are complex retroviruses. Therefore, in addition to structural and enzymatic proteins they encode regulatory proteins and also auxiliary proteins, the main subject of this work. HTLV-1 and BLV auxiliary proteins play key roles in viral infection in vivo. Whether the genome of PTLV-3 encodes such proteins was not determined yet. Therefore their characterization was the first goal of my PhD work. We identified in vitro messenger RNAs encoding 3 new putative proteins. Their impact on the PTLV-3 viral life cycle in vitro and their expression in vivo were then investigated. As a second part of this work, we examined the relationship existing between the Vpx HIV-2 auxiliary protein and its ability to interact with a restriction factor named SAMHD-1. Vpx induces SAMHD-1 degradation and the kinetic of such degradation allows the virus to replicate in myeloid cells. Altogether, these projects provide new insights into the understanding of the roles played by retroviral auxiliary proteins in connection with a tight regulation of viral life cycle and an escape from innate immunity

Fujinami sarcoma virus encodes a 140/000 m.w. polypeptide (P140) which has been correlated as the agent of transformation in host chicken fibroblasts and mammalian fibroblasts. To conclusively identify the role of P140 in the transformation process it will be necessary to obtain intact/ purified P140. The availability of an antibody monoclonally specific to the N-terminal gag encoded portion of P140 suggested a one-step immunoaffinity purification of P140. After purification of the antibody out of mouse ascites fluid, by 50% ammonium sulfate fractionation and ion exchange chromatography, antibody was linked to a Sepharose 4-B matrix activated with cyanogen bromide. The anti-pl9 affinity matrix bound intact P140 as a doublet relative to a polyclonal anti-pl9. Chaotropic agents, high pH and low pH treatments all failed to elute the bound P140 from the affinity matrix. Failing the purification of intact P140 a method of partial proteolysis was used to produce varying sized fragments of P140/ with the goal of purifying these fragments for further work on the role of P140. Trypsin alone in a limited proteolysis produced small, unstable peptides too close in size distribution to be effectively purified. Chymotrypsin alone produced a broad range of more stable peptides, with a predominance of a 45,000 m.w. peptide. Chymotrypsin-trypsin consecutive proteolysis produced a very stable 35,000 m.w. peptide. Gel filtration of the chymotryptic peptides was ineffective as the peptides coraplexed and were not fractionated. Ion exchange chromatography fractionated the complexing chymotryptic peptides, making possible the purification of these peptides. The stable 45,000 m.w. peptide retained some kinase activity, as it phosphorylated the substrate enolase, similar to but less intense than intact P140. A 30,000 m.w. peptide only phosphorylating after ion exchange did not phosphorylate enolase. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

Indiana University-Purdue University Indianapolis (IUPUI) / In an effort to advance the methodology in analyzing RNAPII protein-protein interaction network and to determine the role of the CTD in controlling RNAPII transcription, we devised a method to specifically isolate the CTD-associated and CTD-less RNAPII to identify the proteins that interact with both the CTD and the globular core of RNAPII using novel purification scheme coupled to quantitative proteomics.

The human genome comprises 8% sequences of retroviral origin, so-called human endogenous retroviruses (HERVs). Most of these proviral sequences are defective, but some possess open reading frames. They can lead to the formation of viral transcripts, when activated by intrinsic and extrinsic factors. HERVs are thought to play a pathological role in inflammatory diseases and cancer. Since the consequences of activated proviral sequences in the human body are largely unexplored, selected envelope proteins of human endogenous retroviruses associated with inflammatory diseases, namely HERV-K18, HERV-K113, and HERV-Fc1, were investigated in the present study. A formation of glycosylated envelope proteins was demonstrated in different mammalian cell lines. Nevertheless, protein maturation seemed to be incomplete as no transport to the plasma membrane was observed. Instead, the proteins remained in the ER where they induced the expression of genes involved in unfolded protein response, such as HSPA5 and sXBP1. Furthermore, low expression levels of native envelope proteins were increased by codon optimization. Cell-free expression systems showed that both the transcriptional and translational level is affected. By generating different codon-optimized variants of HERV-K113 envelope, the influence of single rare t-RNA pools in certain cell lines was demonstrated. The mRNA secondary structure also appears to play an important role in the translation of the tested viral envelope proteins. In summary, the formation of certain HERV proteins is basically possible. However, their complete maturation and thus full biologic activity seems to depend on additional factors that might be disease-specific and await elucidation in the future.

No / Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host's heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic variation and resistance to infection, as well as negative effects as agents of tumorigenesis and disease. The avian leukosis virus subgroup E family (ALVE) of endogenous viruses of chickens has been used as a model system for studying the effects of ERVs on host physiology, and approximately 30 distinct ALVE proviruses have been described in the Gallus gallus genome. In this report we describe the development of a software tool, which we call Vermillion, and the use of this tool in combination with targeted next-generation sequencing (NGS) to increase the number of known proviruses belonging to the ALVE family of ERVs in the chicken genome by 4-fold, including expanding the number of known ALVE elements on chromosome 1 (Gga1) from the current 9 to a total of 40. Although we focused on the discovery of ALVE elements in chickens, with appropriate selection of target sequences Vermillion can be used to develop profiles of other families of ERVs and TEs in chickens as well as in species other than the chicken. / Financial support was provided by the EW GROUP, as well as grants from the Canada Foundation for Innovation, Canada Research Chairs Program, and the Natural Sciences and Engineering Council of Canada to RGB, and Canada Institutes of Health Research funding to MGIL and CJM.