Hepatitis E virus (HEV) is a major cause of enterically transmitted acute viral hepatitis in developing countries that lack proper hygienic infrastructure. Hepatitis E is globally distributed and has emerged as an important public health disease in both developing and industrialized countries. HEV is a non-enveloped virus carrying a single-stranded positive-sense RNA genome of approximately 7.200 bp in length. The life cycle of HEV is poorly understood due to the lack of an efficient cell culture system. Animal model systems, including non-human primates, swine, and chickens are being used to study some fundamental aspects of the HEV biology. Recently, novel animal strains of rat and rabbit HEV have been discovered, and whose usage as animal model systems needs to be established. HEV infections in pigs and chickens provide excellent model systems to study the replication and pathogenesis aspects of HEV. Recently, we identified a hypervariable region (HVR) in the open reading frame 1 (ORF1) of HEV. The objectives of this dissertation were to utilize chicken and swine model systems to study the role of HVR in HEV infection in vivo, to determine the effects of HVR on replication of HEV in vitro, and to analyze the effect of exchange of HVR among different genotypes on the replication-competency and virion production in vitro. Extensive sequence variability in the HVR among HEV strains of different genotypes prompted us to study the dispensability of this region. Initially we constructed two partial deletion mutants of genotype 1 human HEV, hHVRd1 and hHVRd2, with in-frame deletion of amino acids (aa) 711 to 777 and 747 to 761 in the HVR of a sub-genomic GFP HEV replicon. Expression of enhanced green fluorescent protein by the mutant hHVRd2 confirmed the dispensability of amino acid residues 747-761 of the HVR. To confirm our in vitro results, specific-pathogen-free (SPF) chickens were intra-hepatically inoculated with capped RNA transcripts from three avian HEV HVR-deletion mutants: mutants aHVRd1 (Δ557-585), aHVRd2 (Δ612-641), and aHVRd3 (Δ557-641). Chickens intra-hepatically inoculated with the mutants, aHVRd1 and aHVRd2, developed active viral infection as evidenced by seroconversion, viremia, and fecal virus shedding. Mutant aHVRd3, with a larger HVR deletion, was apparently attenuated in chickens. Additionally, we used the swine model system to further verify our results from the chicken study. The infectivity of four genotype 3 swine HEV HVR-deletion mutants, sHVRd1 (Δ712-790), sHVRd2 (Δ722-781), sHVRd3 (Δ735-765), and sHVRd4 (Δ712-765) constructed using the genotype 3 swine HEV as the backbone was determined in SPF pigs. Pigs intra-hepatically inoculated with capped RNA transcripts from the mutants sHVRd2, sHVRd3, and sHVRd4 developed active viral infection, whereas mutant sHVRd1 (Δ712-790), with a nearly complete HVR deletion, exhibited an attenuation phenotype. The data from these studies indicate that deletions in HVR do not abolish HEV infectivity in vitro or in vivo, although evidence for attenuation was observed for HEV mutants with a larger or nearly complete HVR deletion. To further elucidate the role of HVR in HEV replication, we investigated the effects of serial amino acid deletions in HVR on the replication of HEV. We first constructed a genotype 1 human HEV luciferase replicon by replacing the ORF2 gene that encodes for the capsid protein with the fire fly luciferase reporter gene. Using the backbone of human HEV genotype 1 luciferase replicon, we constructed a series of HVR-deletion mutants with deletions of variable lengths in the HVR. Amino acid deletions Δ711-725, 711-740 and Δ711-750 were engineered at the N-terminus, deletions Δ729-754, Δ721-766, and Δ716-771 were engineered in the central region, and deletions Δ761-775, Δ746-775, and Δ736-775 were engineered at C-terminus of the HVR. The effects of these serial deletions on HEV RNA replication in the human liver carcinoma cell line, Huh7, were examined. Replication levels of mutants carrying these deletions were compared with that of the wild-type HEV in Huh7 cells. We observed that deletions in the HVR did not abolish viral RNA synthesis but substantially reduced the replication levels of viral RNA, as measured by the reporter luciferase activity. To further verify the effects of HVR deletions on viral RNA replication as observed with the genotype 1 human HEV replicon, we subsequently used a genetically-distinct strain of HEV, avian HEV, and constructed an avian HEV sub-genomic luciferase replicon by substituting the ORF2 gene of avian HEV with the fire fly luciferase gene. Avian HEV HVR-deletion mutants Δ557-603, Δ566-595, and Δ573-587 were then engineered using the backbone of avian HEV luciferase replicon. The replication efficiency of the three deletion mutants of avian HEV in chicken liver hepatoma cell line, LMH, was evaluated. Compared with the wild-type avian HEV, the viral RNA synthesis of the avian HEV HVR-deletion mutants was considerably reduced by the HVR deletions. To analyze the impact of the complete HVR deletion on avian HEV infectivity, we constructed an avian HEV mutant with a deletion of the entire HVR region (aaΔ557-603) using the avian HEV infectious cDNA clone as the backbone. After confirming the viability of the complete HVR-deletion mutant in LMH cells, SPF chickens were intrahepatically inoculated with capped RNA transcripts generated from the mutant. None of the chickens inoculated with the complete HVR-deletion mutant showed evidence of HEV infection, indicating that drastic reduction in replication levels due to complete HVR deletion has resulted in the loss of virus infectivity. The results indicated that HVR may have critical residues that may interact with viral/and or host factors and modulate the replication efficiency of HEV. In the final part of the dissertation research, we sought to determine if the variable sequences of HVR are genotype-specific for in vitro virus replication. By using the genotype 1 human HEV as the backbone, we swapped the HVR of genotype 1 human HEV with the HVRs of the genotype 3 swine HEV and the distantly-related avian HEV to construct two inter-genotypic chimeras, pSKHEV2-Sw and pSKHEV2-Av. Similarly, by using the genotype 3 swine HEV as the backbone, the HVR of genotype 3 swine HEV was swapped with the HVR of genotype 1 human HEV to construct the chimera, pSHEV3-Hu. The viability of these chimeras was tested in Huh7 cells that are permissive for HEV replication. Immunofluorescence assay (IFA) with anti-HEV antibodies revealed that all the three chimeras were replication-competent in Huh7 cells. The infectivity of these chimeras was subsequently evaluated in HepG2 cells. The results showed that exchange of the HVR between different genotypes of mammalian HEVs does not abolish the replication competency and infectivity of HEV. This finding suggests that HVR is not genotype-specific with respect to viral replication and infectivity. The absence of detectable viral antigen in HepG2 cells infected with chimera pSKHEV2-Av suggested a functional incompatibility of the HVR of avian HEV in the mammalian HEV genome. In summary, we identified a highly variable sequence, HVR, in the ORF1 of the HEV genome, and the sequences of the HVR vary significantly among HEV strains of different genotypes. We found that the HVR contain sequences that are dispensable for virus infectivity both in vitro and in vivo. Deletion analysis of HVR revealed that the region may play a role in modulating the replication efficiency of HEV RNA by interacting with viral and/or host factors. Finally, we demonstrated that HVR is not genotype-specific for virus replication and the region can be functionally replaced between mammalian HEV genotypes for virus replication and virion production in vitro. The results from this dissertation research have important implications for better understanding the biology and mechanism of HEV replication and may aid in our efforts to eventually develop a modified live-attenuated vaccine against HEV. / Ph. D.

HEV is an important public health concern due largely to water-borne outbreak. Recent research confirms individual cases of zoonotic transmission due to human exposure to contaminated animal meats. At least four recognized and two putative genotypes of mammalian HEV have been reported: genotypes 1 and 2 are restricted to humans whereas genotypes 3 and 4 are zoonotic. In addition to humans, strains of HEV have been genetically identified from pigs, chickens, rats, mongoose, deer, rabbits and fish. The current experimental vaccines are all based on a single strain of HEV, even though multiple genotypes of HEV are co-circulating in some countries and thus an individual may be exposed to more than one genotype. Therefore, it is important to know if prior infection with a genotype 3 swine HEV will confer protective immunity against subsequent exposure to genotypes 3 and 4 human and swine HEV. In the first study, specific-pathogen-free pigs were divided into 4 groups of 6 each. Pigs in the three treatment groups were each inoculated with a genotype 3 swine HEV, and 12 weeks later, challenged with the same genotype 3 swine HEV, a genotype 3 human HEV, and a genotype 4 human HEV, respectively. Sera from all pigs were tested for HEV RNA and IgG anti-HEV, and fecal samples were also tested for HEV RNA each week. The pigs inoculated with swine HEV became infected as evidenced by fecal virus shedding and viremia, and the majority of pigs also developed IgG anti-HEV prior to challenge at 12 weeks post-inoculation. After challenge, viremia and fecal virus shedding of challenge viruses were not detected, suggesting that prior infection with a genotype 3 swine HEV prevented pigs from developing viremia and fecal virus shedding after challenge with homologous and heterologous genotypes 3 and 4 HEV, respectively. Immunogenic epitopes are located within the open reading frame 2 (ORF 2) capsid protein and recombinant ORF 2 antigens are capable of preventing HEV infection in non-human primates and chickens. In the second study we expressed and purified N-truncated ORF 2 antigens based on swine, rat, and avian HEV strains. Thirty pigs were randomly divided into groups of 6 pigs each and initially vaccinated with 200µg swine ORF 2 antigen, rat ORF 2 antigen, avian ORF 2 antigen, or PBS buffer (positive and negative control groups) and booster with the same vaccine 2 weeks later. At 4 wks, after confirming seroconversion to IgG anti-HEV antibody with ELISA, all groups except the negative control were challenged with swine genotype 3 HEV (administered intravenously). The protective and cross-protective abilities of these antigens were determined following swine genotype 3 challenge by evaluating both serum and fecal samples for HEV RNA using nested RT-PCR and IgG anti-HEV using ELISA. The results from these two studies have important implications for future development of an effective HEV vaccine. As a part of our ongoing efforts to search for potential animal reservoirs for HEV, we tested goats from Virginia for evidence of HEV infection and showed that 16% (13/80) of goat sera from Virginia herds were positive for IgG anti-HEV. Importantly, we demonstrated that selected goat sera were capable of neutralizing HEV in cell culture. Subsequently, in an attempt to genetically identify the HEV-related agent from goats, we conducted a prospective study in a closed goat herd with known anti-HEV seropositivity and monitored a total of 11 kids from the time of birth until 14 weeks of age for evidence of HEV infection. Seroconversion to IgG anti-HEV was detected in 7 out of the 11 kids, although repeated attempts to detect HEV RNA by a broad-spectrum nested RT-PCR from the fecal and serum samples of the goats that had seroconverted were unsuccessful. In addition, we also attempted to experimentally infect laboratory goats with three well-characterized mammalian strains of HEV but with no success. The results indicate that a HEV-related agent is circulating and maintained in the goat population in Virginia and that the goat HEV is likely genetically very divergent from the known HEV strains. / Ph. D.

<p>Hybrid electric vehicles are considered to be an important part of the future vehicle industry, since they decrease fuel consumption without decreasing the performance compared to a conventional vehicle. They use two or more power sources to propel the vehicle, normally one combustion engine and one electric machine. These power sources can be arranged in different topologies and can cooporate in different ways. In this thesis, dynamic models of parallel and series hybrid powertrains are developed, and different strategies for how to control them are compared.An optimization algorithm for decreasing fuel consumption and utilize the battery storage capacity as much as possible is also developed, implemented and tested.</p>

<p>Hybrid electric vehicles have two power sources - an internal combustion engine and an electric motor. These vehicles are of great interest because they contribute to a decreasing fuel consumption and air pollution and still maintain the performance of a conventional car. Different topologies are described in this thesis and especially the series and parallel hybrid electric vehicle and Toyota Prius have been studied. </p><p>This thesis also depicts modelling of a reference car and a series hybrid electric vehicle in Modelica. When appropriate, models from the Modelica standard library have been used. Models for a manual gearbox, final drive, wheel, chassis, air drag and a driver have been developed for the reference car. </p><p>For the hybrid electric vehicle a continuously variable transmission, battery, an electric motor, fuel cut-off function for the internal combustion engine and a converter that distributes the current between generator, electric motor and internal combustion engine have been designed. </p><p>These models have been put together with models from the Modelica standard library to a reference car and a series hybrid electric vehicle which follows the NEDC driving cycle. A sketch for the parallel hybrid electric vehicle and Toyota Prius have also been made in Modelica. </p><p>Developed models have been introduced into the Modelica library VehProLib, which is a vehicle propulsion library under development by Vehicular Systems, Linköpings universitet.</p>

Hybrid electric vehicles are considered to be an important part of the future vehicle industry, since they decrease fuel consumption without decreasing the performance compared to a conventional vehicle. They use two or more power sources to propel the vehicle, normally one combustion engine and one electric machine. These power sources can be arranged in different topologies and can cooporate in different ways. In this thesis, dynamic models of parallel and series hybrid powertrains are developed, and different strategies for how to control them are compared.An optimization algorithm for decreasing fuel consumption and utilize the battery storage capacity as much as possible is also developed, implemented and tested.

Hybrid electric vehicles have two power sources - an internal combustion engine and an electric motor. These vehicles are of great interest because they contribute to a decreasing fuel consumption and air pollution and still maintain the performance of a conventional car. Different topologies are described in this thesis and especially the series and parallel hybrid electric vehicle and Toyota Prius have been studied. This thesis also depicts modelling of a reference car and a series hybrid electric vehicle in Modelica. When appropriate, models from the Modelica standard library have been used. Models for a manual gearbox, final drive, wheel, chassis, air drag and a driver have been developed for the reference car. For the hybrid electric vehicle a continuously variable transmission, battery, an electric motor, fuel cut-off function for the internal combustion engine and a converter that distributes the current between generator, electric motor and internal combustion engine have been designed. These models have been put together with models from the Modelica standard library to a reference car and a series hybrid electric vehicle which follows the NEDC driving cycle. A sketch for the parallel hybrid electric vehicle and Toyota Prius have also been made in Modelica. Developed models have been introduced into the Modelica library VehProLib, which is a vehicle propulsion library under development by Vehicular Systems, Linköpings universitet.

Today uncertainties of petroleum supply and concerns over global warming call for further advancement of green vehicles with higher energy efficiency and lower green house gas (GHG) emissions. Development of advanced hybrid electric powertrain technology plays an important role in the green vehicle transformation with continuously improved energy efficiency and diversified energy sources. The added complexity of the multi-discipline based, advanced hybrid powertrain systems make traditional powertrain design method obsolete, inefficient, and ineffective. This research follows the industrial leading model-based design approach for hybrid electric vehicle powertrain development and introduces the optimization based methods to address several key design challenges in hybrid electric powertrain and its control system design. Several advanced optimization methods are applied to identify the proper hybrid powertrain architecture and design its control strategies for better energy efficiency. The newly introduced optimization based methods can considerably alleviate the design challenges, avoid unnecessary design iterations, and improve the quality and efficiency of the powertrain design. The proposed method is tested through the design and development of a prototype extended range electric vehicle (EREV), UVic EcoCAR. Developments of this advanced hybrid vehicle provide a valuable platform for verifying the new design method and obtaining feedbacks to guide the fundamental research on new hybrid powertrain design methodology. / Graduate

Alphavirus et virus de l'hépatite E, appartiennent à l'alpha-like supergroupe de virus à ARN simple brin positif. Dans cette thèse, la caractérisation fonctionnelle de l'ARNm plafonnement enzyme et le domaine macro sont abordées, afin d'élucider leur rôle dans la réplication virale et de les évaluer en tant que cibles antivirales possibles.Les alphavirus possèdent un mécanisme unique de coiffe de l'ARNm viral impliquant la protéine non structurale nsP1. Nous présentons ici la caractérisation biochimique de nsP1d'alphavirus et son potentiel comme cible antivirale. Pour cela, différents tests enzymatiques ont été développés afin de mieux comprendre et de découpler les différentes étapes de la réaction catalysée par nsP1. Nous avons pu montrer pour la première fois chez les alphaviurs le guanylyltransfert de m7GMP sur l'extrémité 5'-diphosphate d'un ARN. Les techniques développées mises au point ont été mises à profit pour élucider le mode d'action d'une nouvelle classe d'antiviraux d'alphavirus.Le Macro domaine est un domaine protéique ancien et conservé et largement distribué dans tout le règne vivant. Nous déclarons que le domaine Macro de virus de l'hépatite E sert une protéine hydrolase ADP-ribose pour inverser la protéine ADP-ribosylation. L'abolition de l'activité diminue considérablement la réplication d'un réplicon sub-génomique du VHE. L'activité est également présente dans les macro domaines du SRAS-CoV et VEEV. Nos résultats montrent que les macro domaines viraux servent ADP-ribose protéine hydrolase et jouent un rôle important dans la réplication virale, peut-être grâce à la modulation de la réponse antivirale de l'hôte. / Alphavirus and Hepatitis E virus, belong to alpha-like supergroup of positive single stranded RNA viruses. In this thesis, the functional characterization of mRNA capping enzyme and Macro domain are addressed, in order to elucidate their role in the viral replication and to evaluate them as possible antiviral targets. Part I: Alphaviruses are known to possess a unique viral mRNA capping mechanism involving the viral non-structural protein nsP1. Here we report the biochemical characterization and antiviral investigation of alphavirus nsP1. Different enzymatic assays were developed to further understand and uncouple the different reaction steps catalyzed by nsP1. The final guanylyltransfer of m7GMP onto a 5'-diphosphate RNA oligonucleotide was observed for the first time in vitro with an alphavirus nsP1. Taking advantage of the developed techniques, the mode of action of a novel class of alphavirus antivirals, [1,2,3]triazolo[4,5-d]pyrimidin-7(6H)-ones, was deciphered. Part II: Macro domain is an ancient and highly evolutionarily conserved protein domain widely distributed throughout all kingdoms of life. Here, we report that the Macro domain from hepatitis E virus serves as an ADP-ribose protein hydrolase to reverse protein ADP-ribosylation. Abbrogation of this activity dramatically decreases replication of a HEV sub-genomic replicon. This activity is also present in Macro domains from SARS-CoV and VEEV virus. Collectively, our results show that viral Macro domains serve as ADP-ribose protein hydrolase and play important roles in viral replication, possibly through modulating the antiviral host response.

The powertrain design and control strategies for three representative hybrid and plug-in hybrid electric vehicles (HEV/PHEVs), a plug-in hybrid passenger car, a plug-in hybrid race car, and a hybrid electric mining truck, have been investigated through the system modeling, simulation and design optimization. First, the pre-transmission gen-set couple Plug-in Series-Parallel Multi-Regime (SPMR) powertrain architecture was selected for PHEV passenger car. Rule-based load following control schemes based on engine optimal control strategy and Equivalent Consumption Minimization Strategy (ECMS) were used for the operation control of the passenger car PHEV powertrain. Secondly, the rear wheel drive (RWD) post-transmission parallel through road powertrain architecture was selected for race car PHEV. A high level supervisory control system and ECMS control strategy have been developed and implemented through the race car’s on-board embedded controller using dSPACE MicroAutobox II. In addition, longitudinal adaptive traction control has been added to the vehicle controller for improved drivability and acceleration performance. At last, the feasibility and benefits of powertrain hybridization for heavy-duty mining truck have been investigated, and three hybrid powertrain architectures, series, parallel and diesel-electric, with weight adjusting propulsion system have been modeled and studied. The research explored the common and distinct characteristics of hybrid electric propulsion system technology for different vehicular applications, and formed the foundation for further research and development. / Graduate / 0540 / ruicheng@uvic.ca

Georgia Tech has the privilege of competing in EcoCAR 3, a four-year competition in which 16 universities are given a stock 2016 Chevrolet Camaro and work to transform it into a hybrid electric sports car. In this thesis, an overview of the first two years of the author’s work on the team as the Engineering Manager, the graduate student overseeing all vehicle engineering work, will be detailed. The competition will be introduced and described before a discussion on vehicle electrification and the various ways it has been achieved by manufacturers and competition teams. Next, the design of the Georgia Tech vehicle will be presented with a focus on powertrain and supporting component selection. The vehicle model underlying many of these decisions will then be discussed in detail, showing how the team used Simulink and Engineering Equation Solver to effectively predict vehicle performance, emissions, energy consumption, and cooling needs. Building on this, the controls design process known as model/software/hardware in the loop will be discussed in the context of the Georgia Tech team’s use of this process. Finally, a progress update will be given, including photos of the team vehicle in current build state weeks before the Year 2 Competition.