Equine arteritis virus (EAV) is the causal agent of equine viral arteritis (EVA), a disease of equids. Following EAV infection, up to 70% of stallions may become carriers and continuously shed the virus in their semen for varying time periods. The long-term carrier stallion has an important role in the transmission and maintenance of EAV in horse populations. Recently, it has been demonstrated a correlation between in vitro susceptibility of CD3+ T lymphocytes to EAV infection and establishment of long-term persistent infection among stallions following natural infections. In this study, we investigated whether stallions with in vitro EAV susceptible CD3+ T lymphocytes are at higher risk of becoming long-term carriers compared to those with the resistant phenotype following experimental infection with the KY84 strain of EAV. Furthermore, we investigated whether there is a significant effect of EAV infection on semen quality during acute phase of the infection. The data suggested that the establishment of the long-term carrier state seems to be associated with the in vitro CD3+ T lymphocyte susceptible phenotypes and that reduced semen quality resulted from the combined effect of fever and scrotal edema observed following EAV infection rather than the direct effect of the virus.

In this paper, we investigate three particular algorithms: A sto- chastic simulation algorithm (SSA), and explicit and implicit tau-leaping al- gorithms. To compare these methods, we used them to analyze two infection models: A Vancomycin-resistant enterococcus (VRE) infection model at the population level, and a Human Immunode ciency Virus (HIV) within host in- fection model. While the rst has a low species count and few transitions, the second is more complex with a comparable number of species involved. The relative effciency of each algorithm is determined based on computational time and degree of precision required. The numerical results suggest that all three algorithms have the similar computational effciency for the simpler VRE model, and the SSA is the best choice due to its simplicity and accuracy. In addition, we have found that with the larger and more complex HIV model, implementation and modication of tau-Leaping methods are preferred.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

A dengue é uma infecção viral sistêmica que pode se manifestar clinicamente de diversas formas, desde febres leves a hemorragia e síndrome do choque, condições potencialmente fatais. Diversos estudos já foram publicados investigando as mudanças globais de expressão que ocorrem durante a evolução da doença nesses diferentes quadros clínicos. Porém, nenhum desses estudos analisou o papel dos RNAs não codificadores longos (lncRNAs) na progressão da doença. Neste projeto, foi realizada uma metanálise dos dados de expressão provenientes desses estudos de dengue focando na expressão de lncRNAs e seus possíveis mecanismos de regulação gênica. Foram identificados dezenas de lncRNAs cuja expressão aumenta ou diminui em pacientes infectados com dengue comparado com pessoas saudáveis. Através de análise de \"guilty-by-association\", procurou-se identificar genes codificadores de proteína possivelmente regulados por esses lncRNAs ou genes que os regulem. Nossos resultados fornecem evidência de novos mecanismos de regulação entre lncRNAs e mRNAs. / Dengue fever is a systemic viral infection that can manifest clinically in a variety of ways, from mild fever to potentially fatal conditions such as hemorrhage and shock syndrome. Several studies have already been published investigating the global changes in expression that occur during the evolution of the disease in these different clinical settings. However, none of these studies analyzed the role of long non-coding RNAs (lncRNAs) in disease progression. In this project, we performed a meta-analysis of transcriptome data obtained from these dengue studies and focused on the expression of lncRNAs and their possible mechanisms of gene regulation. Dozens of lncRNAs have been identified whose expression increases or decreases in patients infected with dengue compared to healthy individuals. Through guilty-by-association analysis, we identified several lncRNAs that possibly regulate protein coding genes. Our results provide evidence of novel regulatory mechanisms between lncRNAs and mRNAs.

A dengue é uma infecção viral sistêmica que pode se manifestar clinicamente de diversas formas, desde febres leves a hemorragia e síndrome do choque, condições potencialmente fatais. Diversos estudos já foram publicados investigando as mudanças globais de expressão que ocorrem durante a evolução da doença nesses diferentes quadros clínicos. Porém, nenhum desses estudos analisou o papel dos RNAs não codificadores longos (lncRNAs) na progressão da doença. Neste projeto, foi realizada uma metanálise dos dados de expressão provenientes desses estudos de dengue focando na expressão de lncRNAs e seus possíveis mecanismos de regulação gênica. Foram identificados dezenas de lncRNAs cuja expressão aumenta ou diminui em pacientes infectados com dengue comparado com pessoas saudáveis. Através de análise de \"guilty-by-association\", procurou-se identificar genes codificadores de proteína possivelmente regulados por esses lncRNAs ou genes que os regulem. Nossos resultados fornecem evidência de novos mecanismos de regulação entre lncRNAs e mRNAs. / Dengue fever is a systemic viral infection that can manifest clinically in a variety of ways, from mild fever to potentially fatal conditions such as hemorrhage and shock syndrome. Several studies have already been published investigating the global changes in expression that occur during the evolution of the disease in these different clinical settings. However, none of these studies analyzed the role of long non-coding RNAs (lncRNAs) in disease progression. In this project, we performed a meta-analysis of transcriptome data obtained from these dengue studies and focused on the expression of lncRNAs and their possible mechanisms of gene regulation. Dozens of lncRNAs have been identified whose expression increases or decreases in patients infected with dengue compared to healthy individuals. Through guilty-by-association analysis, we identified several lncRNAs that possibly regulate protein coding genes. Our results provide evidence of novel regulatory mechanisms between lncRNAs and mRNAs.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Rhabdoviridae family viruses attacking the plant hosts were only described at the angiosperms. In this work, a gymnosperm rhabdoviridae infection was described for the first time ever ? specifically at Ginkgo biloba. Even though there were not observed any kinds of obvious infection symptoms on any of randomly chosen plant samples, through the molecular methods and detection primers the rhabdoviridae infection was proved at six of the plant samples. The acquired nucleotide and amino acid sequences, which were compared with the GenBank sequences, confirm the Rhabdoviridae family viruses occurrence. These given sequences demonstrated a certain analogy with a Strawberry crinkle virus assigned to the genus of Cytorhabdoviruses. The analyses proved a different reciprocal homology among the nucleotide sequences of the individual isolates, and in all likelihood an occurrence of two up to now unknown viruses in the Ginkgo biloba samples was proved for the first time. A definite categorization will be dependent on an acquisition and comparison of other sequences from the isolates genome and also on certain biological characteristics observation.

Made available in DSpace on 2015-03-26T13:37:50Z (GMT). No. of bitstreams: 1 texto completo.pdf: 864310 bytes, checksum: 5681c5c23525796c1b07e3912abf4732 (MD5) Previous issue date: 2012-07-20 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / During coevolution, plant viruses have developed the ability to modulate the expression of several host genes, or to alter the function of cognate protein to succeed in their multiplication and perpetuation. These virus-induced changes might lead to a high level of dependency, creating an indissoluble link between virus and host. The objective of this study was to investigate the contribution of a DnaJ of Nicotiana benthamiana (homologous of the tomato protein) and of the TCTP protein from tomato during PepYMV infection. These two genes were identified as differentially expressed in a cDNA library constructed from tomato plants infected by PepYMV. Kinetic studies of DnaJ expression in PepYMV-infected N. benthamiana demonstrated that the induction occurs at both 72 hours post-inoculation (hpi) and 14 days post-inoculation (dpi). Plants of N. benthamiana silenced for DnaJ by means of VIGS and tomato plants cv. Moneymaker silenced by transgenesis for TCTP were obtained and mechanically inoculated with PepYMV. Viral infection was confirmed by ELISA and viral load determined by qRT-PCR. Silencing of the DnaJ gene in N. benthamiana interfered with the early stages of viral infection (72 hpi) but its effect on established infections (14dpi) was inconclusive. Non-transformed tomato plants showed severe symptoms of the disease, while TCTP-silenced transgenic plants showed greatly attenuated symptoms or remained asymptomatic. Viral load was dramatically reduced in silenced plants. The subcellular localization of a TCTP-GFP fusion protein in healthy or PepYMV-infected N. benthamiana plants was analyzed by confocal microscopy. In healthy plants TCTP was nuclear and cytoplasmic, while in infected plants at 14 dpi, its subcellular localization was exclusively cytoplasmic. Together, these results suggest that both TCTP and DnaJ are proteins which positively regulate the infection cycle of PepYMV, being required for disease development in the case of TCTP or for the rapid establishment of viral infection in the case of DnaJ. Further studies should be conducted in order to unravel the mechanisms by which these host factors are used to benefit the viral infection. / Durante a coevolução, os vírus de plantas desenvolveram a capacidade de modular a expressão de alguns genes do hospedeiro, ou alterar a função cognata de proteínas para obter sucesso em sua multiplicação e perpetuação. Essas alterações induzidas pelos vírus podem culminar em elevados níveis de especialização, tornando o vínculo com seus hospedeiros indissociável. O objetivo deste trabalho foi investigar a contribuição de uma DnaJ de Nicotiana benthamiana homóloga de tomateiro e da proteína TCTP de tomateiro durante a infecção pelo potyvírus PepYMV. Esses dois genes foram identificados como diferencialmente expressos em uma biblioteca de cDNA construída a partir de tomateiro infectado pelo PepYMV. Estudos de cinética de expressão do gene DnaJ em N. benthamiana infectadas pelo PepYMV demonstraram que a indução do gene ocorre 72 horas pós-inoculação (hpi) e aos 14 dias pós-inoculação (dpi). Plantas de N. benthamiana silenciadas para DnaJ por meio de VIGS e de tomateiro cv. Moneymaker silenciadas por transgenia para o gene TCTP foram obtidas e inoculadas mecanicamente com o PepYMV. A infecção viral foi confirmada por ELISA e a carga viral determinada por qRT-PCR. O silenciamento do gene DnaJ em N. benthamiana interferiu nos estágios iniciais da infecção viral (72 hpi), porém seu efeito em infecções já estabelecidas (14dpi) foi inconclusivo. Plantas não-transformadas de tomateiro exibiram sintomas severos da doença, enquanto as plantas transgênicas silenciadas para o gene TCTP apresentaram sintomas muito atenuados ou permaneceram assintomáticas. Nas plantas silenciadas a carga viral foi drasticamente reduzida. A localização subcelular de TCTP fusionada à proteína GFP em plantas de N. benthamiana sadias ou infectadas pelo PepYMV foi analisada por microscopia confocal. Em plantas sadias a localização de TCTP foi nuclear e citoplasmática, porém em plantas infectadas aos 14dpi, a localização de TCTP foi exclusivamente citoplasmática. Os resultados obtidos sugerem que tanto TCTP quanto DnaJ são proteínas que regulam positivamente o ciclo de infecção do PepYMV, sendo necessárias para o desenvolvimento da doença no caso de TCTP, ou para o rápido estabelecimento da infecção no caso de DnaJ. Estudos posteriores devem ser conduzidos afim de descobrir o mecanismo pelo qual esses fatores do hospedeiro são utilizados em benefício da infecção viral.

Human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infections induce a myriad of disturbances to CD4 T cell functions, including mitochondrial compromise, excessive inflammation, increased telomeric DNA damage and attrition, cellular exhaustion and senescence, and accelerated aging. In this dissertation, the mechanisms underlying metabolic failure, accelerated aging, and cellular dysfunctions were evaluated in CD4 T cells from healthy subjects (HS) treated with a telomere-targeting drug (KML001) or HCV-infected individuals or people living with HIV (PLHIV) compared to HS. We observed that KML001-induced telomere injury resulted in mitochondrial swelling and decreased mitochondrial membrane potential, cellular respiration, mitochondrial DNA (mtDNA) copy number, and ATP production mediated by p53-mediated repression of the master mitochondrial regulators peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) and nuclear respiratory factor 1 (NRF-1). We then investigated the mechanisms responsible for T cell dysfunction and metabolic failure during chronic viral infections (HCV, HIV). We observed that chronic HCV infection leads to elevated production of cellular and mitochondrial reactive oxygen species (ROS), impaired mtDNA, and altered levels of proteins responsible for mediating oxidative stress, apoptosis, and mtDNA maintenance, as well as mitochondrial regulators PGC-1α and mitochondrial transcription factor A (mtTFA), contributing to impaired cellular respiration and mtDNA content. Similarly, we demonstrated that latent HIV infection induced disruptions to CD4 T cell homeostasis and increased cellular exhaustion, senescence, and apoptosis and reduced proliferation. We also observed significant repression of mitochondrial respiration, mtDNA content, and mtTFA levels in CD4 T cells from PLHIV, which was reversed via ectopic expression of mtTFA. Finally, we observed elevated cellular and mitochondria ROS production in CD4 T cells from PLHIV, along with significant deregulation of levels of antioxidant defense (superoxide dismutase 1, SOD1) and oxidative stress-induced DNA damage repair (apurinic/apyrimidinic endonuclease 1, APE1) proteins, which were shown to be essential for cellular respiration independently of mtDNA content. Taken together, this research highlights novel multi-leveled mechanisms by which chronic viral infection induces accelerated T cell aging and mitochondrial compromise via deregulating master mitochondrial regulators and provides a diverse collection of novel therapeutic targets that may be applied to various infectious diseases.

Inflammation in meninges and/or brain is regularly noticed in red foxes and other wild carnivores during rabies control programs. Despite negative rabies virus (RABV) results, the etiologies of these cases remain unknown. Thus, the aim of this study was to provide an overview of the occurrence of pathogens that may cause diseases in the brains of wild carnivores and pose a risk to humans and other animals. In addition to RABV and canine distemper virus (CDV), a variety of pathogens, including members of Flaviviridae, Bornaviridae, Herpesviridae, Circoviridae, as well as bacteria and parasites can also cause brain lesions. In 2016 and 2017, brain samples of 1,124 wild carnivores were examined by direct fluorescent antibody test for RABV as well as (reverse-transcriptase) quantitative polymerase chain reaction (PCR) for the presence of CDV as part of a monitoring program in Saxony-Anhalt, Germany. Here, we applied similar methods to specifically detect suid herpesvirus 1 (SuHV-1), West Nile virus (WNV), Borna disease virus 1 (BoDV-1), canid alphaherpesvirus 1 (CaHV-1), canine parvovirus type 2 (CPV-2), fox circovirus (FoxCV), and Neospora caninum (N. caninum). Further, bacteriogical examination for the existence of Listeria monocytogenes (L. monocytogenes) and immunohistochemistry of selected cases to detect Toxoplasma gondii (T. gondii) antigen were performed. Of all pathogens studied, CDV was found most frequently (31.05%), followed by FoxCV (6.80%), CPV-2 (6.41%), T. gondii (4/15; 26.67%), nematode larvae (1.51%), L. monocytogenes (0.3%), and various other bacterial pathogens (1.42%). In 68 of these cases (6.05%), multiple pathogen combinations were present simultaneously. However, RABV, WNV, BoDV-1, SuHV-1, CaHV-1, and N. caninum were not detected. The majority of the histopathological changes in 440 animals were inflammation (320/440; 72.73%), predominantly non-suppurative in character (280/320; 87.50%), and in many cases in combination with gliosis, satellitosis, neuronophagia, neuronal necrosis, and/or vacuolization/demyelination, or in single cases with malacia. Thus, it could be shown that wild carnivores in Saxony-Anhalt are carriers mainly for CDV and sometimes also for other, partly zoonotic pathogens. Therefore, the existing monitoring program should be expanded to assess the spill-over risk from wild carnivores to humans and other animals and to demonstrate the role of wild carnivores in the epidemiology of these zoonotic pathogens.