La diversité génétique du virus de l'immunodéficience humaine, le VIH-1 responsable de la pandémie du SIDA, représente un challenge dans le développement d'un vaccin qui doit conférer une protection contre différentes formes du virus pour être efficace. L'identification de populations de lymphocytes T CD8+ (CTL) capables de reconnaître des variants peptidiques d'un épitope est donc une étape importante. Dans le modèle singes rhésus, j'ai montré en utilisant des tétramères spécifiques de 9 variants peptidiques d'un épitope qu'une même population de CTL générés par la vaccination, peut reconnaître l'épitope relatif à l'immunogène et un certain nombre de ses variants provenant de diverses formes du VIH-1. Ces études ont également permis de caractériser les populations de CTL spécifiques de chaque variant de cet épitope en analysant l'expression des différents gènes codant pour la chaîne variable β du TCR (Vβ répertoire) et par un large séquençage des régions complémentaires déterminantes 3 (CDR3) du TCRβ. Ces travaux ont montré qu'une vaccination utilisant la séquence du clade C de l'enveloppe du VIH-1 conduit à des réponses divergentes chez 2 singes rhésus Mamu-A*01+. De plus, ces résultats ont mis en évidence que l'usage de certainβes nVe permet pas de déterminer le potentiel cross-réactif des CTL. Par ailleurs, une immunisation utilisant des séquences de l'enveloppe du clade B du VIH-1 peut générer des CTL capables de reconnaître un large nombre de variants de l'épitope testé. L'analyse de 8112 séquences CDR3 du TCRβ a permis de les caractériser. Cependant, les tests fonctionnels ont démontré que bon nombre de ces variants peptidiques stimulent une production suboptimale de cytokines par les CTL générés après vaccination. Ces résultats démontrent que la reconnaissance de variant peptidiques d'un épitope est nécessaire mais pas suffisante pour protéger contre différentes formes du VIH-1 exprimant ces séquences. L'identification de variants peptidiques capables d'induire une réponse fonctionnelle des CTL pourrait contribuer au développement d'un vaccin efficace contre le VIH-1. / The sequence diversity of HIV-1 presents a challenge for the development of an effective vaccine, since such a vaccine must confer protection against diverse forms of the virus. Identifying CD8+ T lymphocytes (CTL) recognizing variants of an epitope sequence is an important step. In the rhesus monkey model, I showed by tetramer binding assays, that the same vaccine elicited CD8+ T lymphocyte populations comparably recognize the epitope relative to the immunogen and a number of variant epitope peptides from diverse forms of HIV-1. During my thesis, I also characterized populations of CD8+ T ymphocytes specific for each variant of the tested epitope by studying their Vβ repertoire and by a large sequencing of the complementarity determining region (CDR3) of the TCRβ. These studies showed that a single clade C env immunization generate CTL with differences in the ability to cross-react to variant epitope in monkeys sharing the same MHC class-Imolecule. Moreover, the data showed that Vβ employed by CTL can not predict the capacity of these CTL to recognize epitopes from diverse HIV-1 isolates. Additionally, I showed that clade B Env immunizations generate populations of CTLrecognizing wild type and a number of variant epitope peptides. However, functional assays demonstrate that many of them stimulate suboptimal cytokine production by the vaccineelicited CTL. These finding demonstrate that the recognition of variant epitope peptides is necessary but not sufficient to protect against different forms of HIV-1. Identifying variant epitopesinducing functional responses of CTL should contribute to the development of an effective vaccine.

<p>Southern Africa is facing one of the most serious HIV epidemics. This project contributes to the HIVNET, Network for Prevention Trials cohort for vaccine development. HIV’s biology and rapid mutation rate have made vaccine design difficult. We examined HIV-1 subtype C diversity and how it relates to CTL epitope location along viral gag sequences. We found a negative correlation between codon sites under positive selection and epitope regions / suggesting epitope regions are evolutionarily conserved. It is possible that epitopes exist in non-conserved regions, yet fail to be detected due to the reference strain diverging from the circulating viral population. To test if CTL clustering is an artifact of the reference strain, we calculated differences between the gag codons and the reference strain. We found a weak negative correlation, suggesting epitopes in less conserved regions maybe evading detection. Locating conserved and optimal epitopes that can be recognized by CTLs is essential for the design of vaccine reagents.</p>

<p>This thesis describes an optimising compiler for translating from SMV to CLP(B). The optimisation is aimed at reducing the number of required variables in order to decrease the size of the resulting BDDs. Also a partitioning of the transition relation is performed. The compiler uses an internal representation of a FSM that is built up from the SMV description. A number of rewrite steps are performed on the problem description such as encoding to a Boolean domain and performing the optimisations. </p><p>The variable reduction heuristic is based on finding sub-circuits that are suitable for reduction and a state space search is performed on those groups. An evaluation of the results shows that in some cases the compiler is able to greatly reduce the size of the resulting BDDs.</p>

More than 50 percent of the land area of the Nordic countries Finland, Norway, and Sweden are covered by dense forests and they are among the most important producers of forest products in the world. Forestry in these countries is based on sustainable management principles – reforestation follows harvesting. Furthermore, increasing demands for more gentle techniques and technologies with less negative impact on the environment ask for development and implementation of new processes and new machine solutions. The increasing interest in developing forest management approaches that are based on gentleness to the environment requires better understanding of the interaction between the forestry machines and the terrain in the harvesting process. / <p>QC 20150827</p> / Gentle Forest Machines

HIV-1 genetic diversity is a major obstacle for developing an effective vaccine. My hypothesis is that HIV-1 genetic diversity can be characterized and that cross-clade immunogens can be predicted at the population level. I systematically investigated positive selection (PS) pressures on HIV-1 Env and Gag proteins based on the analysis of the sequences collected from the Los Alamos Sequence Database. I identified PS sites, investigated PS patterns, correlated PS with the known functional sites of the two proteins, calculated frequencies of HLA alleles targeting CTL epitopes, and compared PS patterns among major subtypes. The results showed that PS pressure was widely dispersed across the entire regions of both HIV-1 Env and Gag proteins, suggesting the conserved regions are under host immune response pressure. The neutralizing antibody, non-neutralizing antibody, and CTL responses were found to be the major forces driving genetic diversity of HIV-1 env and gag genes at population level. However, PS pressures on both Env and Gag proteins remain stable over time, suggesting genetic diversity of HIV-1 driven by host immune responses changed very little over the last 29 years. Furthermore, the results also demonstrated that up to 70% PS sites were shared among the major HIV-1 clades, implying the existence of cross-clade immunogenicity. A number of potential cross-clades immunogens were predicted to elicit CTL or neutralizing antibody responses from Env and Gag proteins. I also detected a significant correlation between HLA allele frequencies and host CTL responses elicited by Accessory/Regulator’s proteins at population level. Moreover, I detected an association between the frequency of HLA-B7 supertype and the number of identified optimal CTL epitopes. The results suggest HLA class I allele frequencies in a population influence the evolution of HIV-1. I also systematically evaluated the utility of ultra-deep pyrosequencing to characterize genetic diversity of HIV-1 gag genes within quasispecies. The results showed that ultra-deep pyrosequencing of amplified HIV genes is a better method than the traditional Sanger-clone-based method in the comprehensive characterization of genetic diversity of HIV-1 quasispecies, especially in detecting low frequency variations. In conclusion, my thesis provides important information for rational design of an effective HIV-1 vaccine.

La diversité génétique du virus de l'immunodéficience humaine, le VIH-1 responsable de la pandémie du SIDA, représente un challenge dans le développement d'un vaccin qui doit conférer une protection contre différentes formes du virus pour être efficace. L'identification de populations de lymphocytes T CD8+ (CTL) capables de reconnaître des variants peptidiques d'un épitope est donc une étape importante. Dans le modèle singes rhésus, j'ai montré en utilisant des tétramères spécifiques de 9 variants peptidiques d'un épitope qu'une même population de CTL générés par la vaccination, peut reconnaître l'épitope relatif à l'immunogène et un certain nombre de ses variants provenant de diverses formes du VIH-1. Ces études ont également permis de caractériser les populations de CTL spécifiques de chaque variant de cet épitope en analysant l'expression des différents gènes codant pour la chaîne variable β du TCR (Vβ répertoire) et par un large séquençage des régions complémentaires déterminantes 3 (CDR3) du TCRβ. Ces travaux ont montré qu'une vaccination utilisant la séquence du clade C de l'enveloppe du VIH-1 conduit à des réponses divergentes chez 2 singes rhésus Mamu-A*01+. De plus, ces résultats ont mis en évidence que l'usage de certainβes nVe permet pas de déterminer le potentiel cross-réactif des CTL. Par ailleurs, une immunisation utilisant des séquences de l'enveloppe du clade B du VIH-1 peut générer des CTL capables de reconnaître un large nombre de variants de l'épitope testé. L'analyse de 8112 séquences CDR3 du TCRβ a permis de les caractériser. Cependant, les tests fonctionnels ont démontré que bon nombre de ces variants peptidiques stimulent une production suboptimale de cytokines par les CTL générés après vaccination. Ces résultats démontrent que la reconnaissance de variant peptidiques d'un épitope est nécessaire mais pas suffisante pour protéger contre différentes formes du VIH-1 exprimant ces séquences. L'identification de variants peptidiques capables d'induire une réponse fonctionnelle des CTL pourrait contribuer au développement d'un vaccin efficace contre le VIH-1.

Due to the constantly growing environmental concerns about global warming, there is immense pressure on the coal-to-liquids (CTL) industry to lower carbon dioxide emissions. This study evaluates the cogeneration of electricity and process steam, using coal and nuclear heat obtained from a High Temperature Gas Cooled Reactor (HTGR) such as a Pebble Bed Modular Reactor (PBMR), for the use in a CTL plant. Three different cogeneration processes were investigated to resolve what influence nuclear cogenerated electricity and process steam would have on the carbon dioxide emissions and the unit production cost of electricity and process steam. The first process investigated utilises coal as combustion medium and an extraction/condensing steam turbine, together with the thermodynamic Rankine cycle, for the cogeneration of electricity and process steam. This process was used as a basis of comparison for the nuclearbased cogeneration processes. The second process investigated utilises nuclear heat generated by a HTGR and the same power conversion system as the coal-based cogeneration system. Utilising a HTGR as a heat source can decrease the carbon dioxide emissions to approximately zero, with a 91.6% increase in electricity production cost. The last process investigated is the nuclear-based closed cycle gas turbine system where a gas turbine and Brayton cycle is coupled with a HTGR for the cogeneration of electricity and process steam. It was found on technical grounds that this process would not be viable for the cogeneration of electricity and process steam. The unit production cost of electricity and process steam generated by each process were determined through an economic analysis performed on each process. Overall it was found that the CTL industry could benefit a great deal from utilising nuclear heat as a heat source. / Thesis (M.Ing. (Nuclear Engineering))--North-West University, Potchefstroom Campus, 2012.

HIV-1 genetic diversity is a major obstacle for developing an effective vaccine. My hypothesis is that HIV-1 genetic diversity can be characterized and that cross-clade immunogens can be predicted at the population level. I systematically investigated positive selection (PS) pressures on HIV-1 Env and Gag proteins based on the analysis of the sequences collected from the Los Alamos Sequence Database. I identified PS sites, investigated PS patterns, correlated PS with the known functional sites of the two proteins, calculated frequencies of HLA alleles targeting CTL epitopes, and compared PS patterns among major subtypes. The results showed that PS pressure was widely dispersed across the entire regions of both HIV-1 Env and Gag proteins, suggesting the conserved regions are under host immune response pressure. The neutralizing antibody, non-neutralizing antibody, and CTL responses were found to be the major forces driving genetic diversity of HIV-1 env and gag genes at population level. However, PS pressures on both Env and Gag proteins remain stable over time, suggesting genetic diversity of HIV-1 driven by host immune responses changed very little over the last 29 years. Furthermore, the results also demonstrated that up to 70% PS sites were shared among the major HIV-1 clades, implying the existence of cross-clade immunogenicity. A number of potential cross-clades immunogens were predicted to elicit CTL or neutralizing antibody responses from Env and Gag proteins. I also detected a significant correlation between HLA allele frequencies and host CTL responses elicited by Accessory/Regulator’s proteins at population level. Moreover, I detected an association between the frequency of HLA-B7 supertype and the number of identified optimal CTL epitopes. The results suggest HLA class I allele frequencies in a population influence the evolution of HIV-1. I also systematically evaluated the utility of ultra-deep pyrosequencing to characterize genetic diversity of HIV-1 gag genes within quasispecies. The results showed that ultra-deep pyrosequencing of amplified HIV genes is a better method than the traditional Sanger-clone-based method in the comprehensive characterization of genetic diversity of HIV-1 quasispecies, especially in detecting low frequency variations. In conclusion, my thesis provides important information for rational design of an effective HIV-1 vaccine.

Due to the constantly growing environmental concerns about global warming, there is immense pressure on the coal-to-liquids (CTL) industry to lower carbon dioxide emissions. This study evaluates the cogeneration of electricity and process steam, using coal and nuclear heat obtained from a High Temperature Gas Cooled Reactor (HTGR) such as a Pebble Bed Modular Reactor (PBMR), for the use in a CTL plant. Three different cogeneration processes were investigated to resolve what influence nuclear cogenerated electricity and process steam would have on the carbon dioxide emissions and the unit production cost of electricity and process steam. The first process investigated utilises coal as combustion medium and an extraction/condensing steam turbine, together with the thermodynamic Rankine cycle, for the cogeneration of electricity and process steam. This process was used as a basis of comparison for the nuclearbased cogeneration processes. The second process investigated utilises nuclear heat generated by a HTGR and the same power conversion system as the coal-based cogeneration system. Utilising a HTGR as a heat source can decrease the carbon dioxide emissions to approximately zero, with a 91.6% increase in electricity production cost. The last process investigated is the nuclear-based closed cycle gas turbine system where a gas turbine and Brayton cycle is coupled with a HTGR for the cogeneration of electricity and process steam. It was found on technical grounds that this process would not be viable for the cogeneration of electricity and process steam. The unit production cost of electricity and process steam generated by each process were determined through an economic analysis performed on each process. Overall it was found that the CTL industry could benefit a great deal from utilising nuclear heat as a heat source. / Thesis (M.Ing. (Nuclear Engineering))--North-West University, Potchefstroom Campus, 2012.

<p>Southern Africa is facing one of the most serious HIV epidemics. This project contributes to the HIVNET, Network for Prevention Trials cohort for vaccine development. HIV’s biology and rapid mutation rate have made vaccine design difficult. We examined HIV-1 subtype C diversity and how it relates to CTL epitope location along viral gag sequences. We found a negative correlation between codon sites under positive selection and epitope regions / suggesting epitope regions are evolutionarily conserved. It is possible that epitopes exist in non-conserved regions, yet fail to be detected due to the reference strain diverging from the circulating viral population. To test if CTL clustering is an artifact of the reference strain, we calculated differences between the gag codons and the reference strain. We found a weak negative correlation, suggesting epitopes in less conserved regions maybe evading detection. Locating conserved and optimal epitopes that can be recognized by CTLs is essential for the design of vaccine reagents.</p>