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This thesis describes the production of adenovirus-based vaccines containing codon-optimized genes from Nipah virus and Crimean-Congo Hemorrhagic Fever virus. Genes encoding envelope proteins from Crimean-Congo Hemorrhagic Fever Virus and Nipah Virus were codon-optimized for translation in human cells and constructed using a modified method of non-gapped gene synthesis, while the entire M segment encoding the glycoprotein precursor for Crimean-Congo Hemorrhagic Fever Virus was commercially synthesized. Genes were cloned into recombinant human adenovirus serotype 5 and the resulting viral particles were amplified, titred and analyzed for in vivo efficacy. Results show that a modified method of non-gapped gene synthesis is an effective and efficient method of producing antigen-encoded DNA and at a fraction of the cost and time required for commercial synthesis. Furthermore, adenovirus-based vaccines induce both cellular and humoral immune responses providing for a highly efficacious vaccine during potential disease outbreaks, where time to completion is of utmost importance. This study has shown that recombinant adenoviral vaccines for Crimean-Congo Hemorrhagic Fever virus and Nipah virus can be produced rapidly and efficiently from virtual DNA sequence to optimized recombinant vaccines in just eight months.

No description available.

Prion diseases are curious neurodegenerative diseases characterized by the conversion of a cellular protein, PrPC, into an infectious isoform, PrPSc. One of the earliest hallmarks of disease and concurrent with prion deposition, is the activation of the brain’s principal immune effector cells, microglia. In prion disease, activated microglia synthesize fairly low levels of pro-inflammatory cytokines, presumably to ameliorate the severe pathology that can arise in host tissue as a result of an acute inflammatory response. The specific stimuli and signaling pathways that lead to this modulation of function are as yet unknown. However, the involvement of miRNAs, a recently identified class of regulatory molecules, is likely. Recently, miR-146a was found to be upregulated in the brains of prion infected mice. In addition, its expression was found to be enriched in cells of microglial origin. It was hypothesized that, given the immunomodulatory role ascribed to miR-146a in macrophages, upregulation of miR-146a may function to attenuate the microglial immune response to prion infection. The first objective was to identify inflammatory related miRNAs associated with prion disease in microglia. Using Taqman Low Density Arrays, allowing for the detection of hundreds of miRNAs at once, the miRNAs of microglia treated with inflammatory agonists were profiled. The miRNA profile of activated microglia was found to be similar to that of macrophages. Furthermore, among the miRNAs profiled, miR-146a and miR-155 were the most highly induced and persistently expressed over 24 hours. The second objective was to investigate miR-146a induction. Therefore, microglia were treated with various agonists and miR-146a expression was determined using Taqman miR-146a assays. Although treatment with a PrP-mimic did not induce miR-146a expression, stimulation of TLRs 1, 2, 4, and 5, resulted in significant over-expression similar to what has been described previously. Moreover, in contrast to the rapid and transient induction of inflammatory mediators, miR-146a follows alternate kinetics functioning to prolong the dampening of the innate immune response following activation via TLR4 and TLR2. By employing a functional proteomic strategy, the third objective was to identify miR-146a regulated proteins. First, miR-146a expression was manipulated using miR-146a mimics and miR-146a inhibitors. Secondly, the functional model was validated by confirming decreased expression of IL6 by ELISA in miR-146a over-expressing microglia cells. Lastly, using Tandem Mass Tag labels to discriminate between treatment group (miR-146a mimic and TLR2 agonist) and control group (scrambled-miR and TLR2 agonist), the effect of miR-146a on the proteome was determined. In total, 172 proteins were identified as being miR-146a regulated and gene ontology assignment resulted in an over-representation of proteins involved in cellular dynamics capable of altering the activation state of microglia. After filtering for bioinformatically predicted targets and those implicated in a similar genomic study, it was decided to further investigate proteins ARF6, RhoA and NOS2 based on their role in modulating the phagocytic potential of microglia. The final objective was to validate miR-146a putative direct targets identified from the proteomics analysis. Luciferase expression of the 3’UTR of targets upon transfection with miR-146a were determined. Based on luciferase analysis, NOS2 appears to be directly targeted by miR-146a and this was also confirmed by western blot. While production of NOS2 by microglia under an acute activation state serves to support and protect CNS homeostasis, chronic expression of this factor can lead to neurotoxicity. Therefore, miR-146a appears to have an overarching role in altering microglial activation during prion disease thus protecting neurons from bystander damage. Taken together, these results suggest that miR-146a could play an important role in the prion disease process by specifically attenuating the microglial induced immune response. Therefore, manipulation of miR-146a may represent a novel therapeutic strategy. Furthermore, given that miR-146a de-regulation has been observed in other neurodegenerative diseases, these results may well extend beyond the realm of prion disease. Lastly, although practical limitations relating to the sensitivity of the comparative proteomics methodology meant that it alone were not sufficient to identify miRNA targets, an integrated approach that takes into consideration genomic and bioinformatic strategies is most promising.

The primary adaptive organismal response to stress involves the activation of the hypothalamic-sympathetic-chromaffin cell (HSC) axis leading to rapid secretion of catecholamines, predominantly epinephrine. The hypothalamus-pituitary-interrenal (HPI) axis activation follows, leading to the secretion of cortisol in teleosts. Both these hormones play key roles in fueling the increased energy demand associated with stress. On prolonged exposure to periods of chronic stress, the stress response shifts from adaptive to maladaptive, eventually resulting in decreased disease resistance, reduced growth and an overall decline in fitness. This reduction of performance can be viewed as a consequence of the animals altered energy budget, with an increase in the metabolic requirements to cope with stress, leading to a reduction in body defense and growth potential. However, the mechanisms linking stress effects on growth and immune performance are far from clear. The suppressors of cytokine signalling (SOCS) are gaining increasing attention in mammalian models and particularly in human medicine for their ability to regulate diverse physiological functions like immunity, growth and development. Even though homologues of the SOCS genes have been identified in fishes, their functional roles are unknown. This paucity of information on the role of SOCS, combined with the knowledge that they are key regulators of energy demanding pathways in mammals, led to the hypothesis that the SOCS genes may be playing a critical role during stress to divert energy away from immune and growth processes in fishes. To test this, liver was used as a model because this tissue plays an important role in stress adaptation, immune response and growth. The ability of cortisol to modulate immune responses in the liver was investigated by exposing rainbow trout (Oncorhynchus mykiss) hepatocytes to lipopolysaccharide (LPS), a potent immunostimulant, along with cortisol and mifepristone- a glucocorticoid receptor (GR) antagonist, to tease out the role of cortisol signalling on immune function. The results showed that LPS stimulation increases the cellular stress response and metabolic capacity and induces the expression of innate response mediators in trout hepatocytes. Cortisol modulates these responses and this involves GR signalling. The results demonstrated for the first time that cortisol upregulates SOCS-1 and SOCS-2 mRNA abundance in trout liver, leading to the proposal that these proteins may be involved in stress/cortisol-mediated immune suppression. The SOCS are also potentially involved in energy–reallocations associated with nutritional restriction. To test this, immune responses and SOCS regulation in response to LPS challenge were investigated between two salmonids exhibiting different life-strategies, the anadromous Arctic charr (Salvelinus alpinus), which undergo natural long-term fasting, and the rainbow trout, that do not naturally fast. Arctic charr and rainbow trout were fed or fasted for 85 and 118 d, respectively, and injected with LPS to examine their ability to evoke an immune response despite their negative energy balance. While fasting did not alter stress parameters like plasma cortisol and glucose levels in the Arctic charr, nutrient restriction modified plasma glucose and lactate levels and liver glycogen content in rainbow trout. Additionally the fasted charr showed lower cytokine responses to LPS than the fed charr, while there was no difference in the degree of cytokine responses between the fed and fasted rainbow trout. Fasting also upregulated SOCS isoforms in the Arctic charr, but reduced SOCS-1 expression in rainbow trout. LPS upregulated SOCS-3 in the Arctic charr, but downregulated SOCS-2 levels in rainbow trout. Together, these results suggest differences in the stress, cytokine and SOCS responses to fasting and LPS stimulation between these two salmonid species. Specifically, SOCS upregulation by fasting in charr may be adaptive to restrict energy demanding pathways, including inflammatory response and growth, to cope with the negative energy balance during overwintering. To assess if SOCS are acutely regulated by stress and if this response was modulated by fasting and LPS stimulation, trout were fed or fasted for 118 d and then injected with LPS, and 72 h later subjected to a handling disturbance. Prior fasting and LPS stimulation altered the acute stressor-mediated changes in plasma cortisol, glucose and lactate levels and liver glycogen content and GR expression in trout. Acute stress also modulated liver SOCS-2 and SOCS-3 mRNA levels in rainbow trout. Overall the results suggest that liver SOCS-2 upregulation by acute stress may be playing a role in the metabolic adjustments essential to cope with stress in fishes. Finally, a series of in vitro studies to identify possible mechanisms involved in SOCS mediated immune and growth suppression were carried out. The objective was to examine whether upregulation of SOCS genes, a key negative regulator of JAK/STAT signalling by cortisol, is a key molecular link in the suppression of growth and immune responses during stress in fish. Cortisol exposure suppressed growth hormone (GH)-stimulated insulin like growth factor (IGF-1) expression and this involved reduced STAT5 phosphorylation/ activation and decreased total JAK2 protein levels. Cortisol also suppressed LPS-induced IL-6 transcript levels. While LPS reduced GH signalling, this was mediated by the downregulation of GH receptors and not due to upregulation of SOCS genes. These results highlight a novel molecular mechanism, involving SOCS upregulation by cortisol, linking stress effects on growth and immune suppression in rainbow trout. Altogether, the results for the first time highlight novel functional roles for the SOCS genes as regulators and integrators of stress-immune-growth processes, and the mode of action involves their regulation by cortisol signalling in fishes.

This thesis describes the production of adenovirus-based vaccines containing codon-optimized genes from Nipah virus and Crimean-Congo Hemorrhagic Fever virus. Genes encoding envelope proteins from Crimean-Congo Hemorrhagic Fever Virus and Nipah Virus were codon-optimized for translation in human cells and constructed using a modified method of non-gapped gene synthesis, while the entire M segment encoding the glycoprotein precursor for Crimean-Congo Hemorrhagic Fever Virus was commercially synthesized. Genes were cloned into recombinant human adenovirus serotype 5 and the resulting viral particles were amplified, titred and analyzed for in vivo efficacy. Results show that a modified method of non-gapped gene synthesis is an effective and efficient method of producing antigen-encoded DNA and at a fraction of the cost and time required for commercial synthesis. Furthermore, adenovirus-based vaccines induce both cellular and humoral immune responses providing for a highly efficacious vaccine during potential disease outbreaks, where time to completion is of utmost importance. This study has shown that recombinant adenoviral vaccines for Crimean-Congo Hemorrhagic Fever virus and Nipah virus can be produced rapidly and efficiently from virtual DNA sequence to optimized recombinant vaccines in just eight months.

This thesis presents studies on the interaction between the human T cell lymphotropic virus type 1 (HTLV-1) Tax protein and the 20S proteasome and the role of the interaction in cellular processes and the cytotoxic T cell (CTL) response against HTLV-1. The rapid translocation of Tax into the nucleus is described. Tax accumulates in the nucleus and forms unique bodies involved in transcriptional activation. It was further found that Tax associated with assembled nuclear 20S proteasomes and stimulated the chymotryptic and tryptic activities of the 20S proteasome, independent of the induction of the LMP2 and LMP7 proteasome subunits. Confocal microscopy revealed a partial colocalisation of Tax with nuclear proteasomes. A panel of Tax mutants was generated and their subcellular localisation and association with the 20S proteasome analysed. This analysis revealed that both the N- and C-terminus of Tax play a role in proteasome binding of Tax and further showed that proteasome binding was not sufficient for nuclear localisation of Tax. Therefore, Tax probably translocates into the nucleus prior to and independent of proteasome association. Tax specific CTL clones were generated and characterised using tetrameric MHC class I/peptide complexes. These CTL clones were used to investigate the requirements for processing and presentation of Tax for recognition by CTL. It was found that Tax was a metabolically very stable protein and that the presentation of the immunodominant Tax 11-19 epitope was dependent on the transporter associated with antigen presentation (TAP), independent of the expression of LMP2 and LMP7 proteasome subunits and resistant to treatment with the proteasome inhibitor lactacystin. It is proposed that the interaction between Tax and the 20S proteasome plays a role in Tax mediated transcriptional activation, leading to cellular activation and proliferation, and may not determine the immunodominance of Tax in the CTL response against HTLV-1.

<p>The activation and maintenance of plant immune responses require a significant amount of energy because they are accompanied by massive transcriptional reprogramming. Spurious activation of plant defense machinery can lead to autoimmune diseases and growth inhibition. So it is important for plants to tightly regulate the immune system to ensure the balance between growth and defense. However, neither the molecular mechanisms nor the design principles of how plants reach this balance are understood. </p><p>In this dissertation work, I showed how transcriptional and translational control of plant immune system can help avoid the constant immune surveillance and elicit a proper level of defense responses when necessary. These fine tunings of the immune system ensure the balance between growth and defense. </p><p>My research on the transcriptional regulation of plant defense responses led to the surprising discovery that even without pathogen, plant can 'anticipate' potential infection according to a circadian schedule under conditions that favor the initiation of infection. Functional analysis of 22 novel immune components unveiled their transient expression at dawn, when the infection is most likely to happen. This pulse expression pattern was shown to be regulated by the central circadian oscillator, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) since these 22 genes are no longer induced in the cca1 mutant. Moreover, the temporal control of the transcription level of these 22 immune genes by CCA1 also fine tunes their expression pattern according to the perceptions of different pathogenic signals. At the basal defense level, the expression of these genes can be transiently induced upon perceptions of critical infection stages of the pathogen. When an elevated level of defense response is needed, the high expression levels of these genes are maintained to confer a stronger immunity against pathogen. Since this stronger form of defense may also cause the suicidal death of the plant cells, the interplay between the circadian clock and defense allows a better decision on the proper level of the immunity to minimize the sacrificial death. The circadian clock is also known to regulate the growth-related cellular functions extensively. So the circadian clock can help to balance the energy used in growth and defense through transcriptional regulation on both sides.</p><p>Besides the integrated control by the circadian clock, the translational control on a key transcription factor involved in the growth-to-defense transition can also maintain the balance between growth and defense.TBF1 is a major transcription factor that can initiate the growth-to-defense transition through transcriptional repression of growth-associated cellular functions and induction of defense-related machinery. Bioinformatics studies identified 2 upstream open reading frames (uORFs) encoding multiple phenylalanine at 5' of the translation initiation codon of TBF1. Under normal conditions, these 2 uORFs can repress the translation of TBF1 to prevent accidental activation. However, pathogen infection may cause rapid and transient depletion of phenylalanine, a well-known precursor for cell wall components and the SAR signal SA. This depletion signal can be reflected by the increase of uncharged tRNAPhe, which subsequently leads to the phosphorylation of eIF2á and the release of uORFs' repression on TBF1. These findings provided the molecular details of how uORF-based translational control can couple transcriptional reprogramming with metabolic status to coordinately trigger the growth-to-defense transition. </p><p>In summary, my dissertation work has identified previously unrecognized regulatory mechanisms by which plant immune responses are balanced with growth. These new findings will further investigations into these novel interfaces between plants and pathogens. Future studies will definitely further improve our understandings of the plant-microbe interactions.</p> / Dissertation

The last decade has been witness to a number of seminal discoveries in the field of innate immunity. The discovery that microbial molecules and endogenous danger signals can be detected by germ-line encoded receptors has changed the way we study the immune system. Indeed, the characterization of Toll in Drosophila as a sensor of microbial products in 1997 then led to the discovery of a family of Toll Like Receptors (TLRs) in mammals. TLRs are critical for the induction of inflammatory responses and the generation of a successful adaptive immune response. The array of ligands that these transmembrane proteins recognized mediates defense against bacteria, viruses, fungus and parasites, as well as, possibly, cancerous cells. In addition to this membrane-bound family of recognition proteins, two families of pattern recognition receptors have been recently shown to respond to microbial and chemical ligands within the cytosol. These represent the Nod Like Receptors (NLRs) and RIGI-like helicase receptor (RLH) families. Nod1 and Nod2 are members of the NLR family of proteins, which are responsible for the recognition of components derived from the bacterial cell wall, more precisely, moieties of peptidoglycan. As such, Nod1 and Nod2 are implicated in the recognition and the defense against bacterial pathogens. Importantly, the genes encoding these two proteins have also been linked to the etiology of several inflammatory disorders such as Crohn’s disease and asthma. In this thesis, we show that recognition of Nod1 and Nod2 ligands generates a rapid and transient inflammatory response in vivo. When co-injected with a model protein, Nod1 and Nod2 ligands exhibit adjuvant properties that lead to the generation of an antigen-specific Th2 type adaptive immune response. Surprisingly, recognition of the Nod1 ligand in non-hematopoietic cells is critical for the generation of this immune response. In contrast, TLRs classically tip the balance towards a Th1 response and interestingly, co-injection of TLR and Nod ligands synergize to generate a more potent immune response characterized by the generation of Th1, Th2 and Th17 T cell respones. To study the role of Nod1 and Nod2 in the context of a bacterial infection in vivo, we used an intestinal mouse pathogen, Salmonella enterica serovar Typhimurium. We were able to show that Nod1-deficient mice, but not Nod2-deficient mice, are more susceptible to the strain of this bacterium, which enters the host through the active pickup in the intestinal lumen by underlying myeloid cells. This sampling mechanism is mediated by a subset of dendritic cells that populate the intestinal lamina propria. Accordingly, the defect seen in Nod1-deficient mice localizes to the mucosal barrier where these dendritic cells appear to have an impaired response towards the bacteria. Taken together, these results increase our knowledge on the general role of Nod1 and Nod2 in immunity and might generate new avenues of research and potential therapeutic targets.