The study of the evolution and phylogeny of West Nile virus (WNV) has been an important area of research since the introduction of WNV in 1999. However, genome sequencing of isolates from the Southeastern part of the United States has been somewhat limited. To determine how WNV has evolved at a more localized level, ten isolates from Florida and Georgia from 2003-2012 were completely sequenced using Illumina's next-generation technology. In addition, a phylogenetic comparison of both the complete genome and select partial genomes was completed to ensure consistency among the results. This study further demonstrated the dominance of the North American WN02 genotype within the Southeastern United States. In addition, phylogenetic analyses revealed the continued presence of genetic variance in 2012 with the finding of a new group within the North American clade. In conclusion, WNV has continued to evolve within the Southeastern US.

This thesis describes aspects of the ecology of West Nile virus (WNV) including factors contributing to the distribution of WNV, possible future distribution, and effects of WNV on host abundance in the Canadian prairies provinces: Alberta, Saskatchewan, and Manitoba. Using mosquito surveillance data collected between 2005 and 2008, models integrating abiotic and biotic factors were constructed to predict the weekly and monthly scales of WNV infection rate in Culex tarsalis, which is the primary vector of WNV in the Canadian prairies. At the weekly scale, the WNV infection rate in Cx. tarsalis increased with increasing Cx. tarsalis abundance and mean temperature lagged from 1 to 8 weeks, but decreased with an increasing mean precipitation lagged from 2 to 6 weeks. Furthermore, precipitation was a ‘distorter variable’ which altered the association between Cx. tarsalis abundance and the WNV infection rate. Study at the monthly scale showed that higher mean temperature and time lagged mean temperature elevated were associated with increased numbers of Cx. tarsalis and higher WNV infection rates. However, increasing precipitation was associated with higher abundance of Cx. tarsalis and lower WNV infection rate. In addition, this study found that increased temperature fluctuation and wetland land cover were associated with decreased WNV infection rate in Cx. tarsalis. Climate change could drive dramatic alterations in the spatial and temporal distribution and overall incidence of vector-borne diseases. The constructed models and biological thresholds were used to predict the distribution of Cx. tarsalis and WNV infection rate in the prairie provinces under a range of potential future climate and habitat conditions. In the current endemic regions, the projected WNV infection rate under the median outcome scenario in 2050 was 18 times higher than under current climate conditions. Seasonal occurence of Cx. tarsalis infected with WNV extended from June to August to include May and September. Moreover, models predicted northward range expansion for Cx. tarsalis and WNV. The declines of susceptible bird abundance caused by WNV may further influence the bird community composition and, in turn, affect the incidence of WNV through a dilution effect. The North American Breeding Bird Survey data was used to evaluate the effect of WNV on the abundance of selected birds in the Canadian prairies, as well as the effects of bird community composition on the WNV risk. There was no significant decline in bird abundances of selected birds following the emergence of WNV. These findings suggest that the effect of WNV on selected bird abundance and bird community composition is insignificant. In addition, there is no evidence to support the association between bird community composition and WNV infection rate in Cx.tarsalis in the Canadian prairies. Lastly, findings in this thesis and current knowledge were integrated to create a decision making flowchart for the prevention of WNV infection in the prairie provinces.

The zoonotic potential of Trichinella zimbabwensis as supported by the clinical symptoms observed in experimentally infected, non-human primates (Mukaratirwa et al., 2001) necessitates research aimed at elucidating the distribution and epidemiology of this parasite. No controlled studies have been conducted to determine the predilection muscles of Trichinella zimbabwensis larvae in Nile crocodiles (Crocodylus niloticus) or the influence of infection intensity on the distribution of the larvae in crocodiles. Neither has the influence of Trichinella zimbabwensis on biochemical parameters in crocodiles been assessed previously. To determine the distribution patterns of Trichinella zimbabwensis larvae and predilection muscles and to assess the influence on selected biochemical parameters, fifteen crocodiles were randomly divided into three cohorts of five animals each to represent high infection (642 larvae/kg of body weight), medium infection (414 larvae/kg of bodyweight) and low infection (134 larvae/kg of bodyweight) cohorts. In the high infection cohort, high percentages of larvae were observed in the tricep muscles (26%) and hind limb muscles (13%). In the medium infection cohort, high percentages of larvae were found in the tricep muscles (50%), sternomastoid (18%) and hind limb muscles (13%). For the low infection cohort, larvae were mainly found in the intercostal muscles (36%), longissimus complex (27%), forelimb muscles (20%), and hind limb muscles (10%). Predilection muscles in the high and medium infection cohorts were similar to those reported in naturally infected crocodiles despite changes in infection intensity. The high infection cohort had significantly higher numbers of larvae in the intercostal, longissimus complex, external tibial flexor, longissimus caudalis and caudal femoral muscles (P < 0.05) compared to the medium infection cohort. In comparison to the low infection cohort, the high infection cohort harboured significantly higher numbers of larvae in all muscles (P < 0.05) except for the tongue and pterygoid. The high infection cohort harboured significantly higher numbers of larvae (P < 0.05) in the sternomastoid, tricep, intercostal, longissimus complex, external tibial flexor, longissimus caudalis and caudal femoral muscles compared to naturally infected crocodiles. The importance of host characteristics in determining predilection and the importance of leg musculature as a predilection site for Trichinella spp. in sylvatic carnivores were both confirmed in this study. Deviations from normal parameters of blood glucose, alanine transaminase (ALT), aspartate transaminase (AST), creatine phosphokinase (CPK) and lactate dehydrogenase (LDH) compared to observations in uninfected reptiles were observed. Hypoglycaemia was not observed in the infected groups in this study. The humoral immune response to Trichinella zimbabwensis infection was evaluated in all three groups by way of indirect ELISA. Peak values of blood glucose, LDH and AST were observed on day 56, 49 and 42 p.i. in the high, medium and low infection cohorts respectively. CPK values peaked on day 35 p.i. in all three cohorts. Peak ALT values were reached on day 56 in the high infection cohort and on day 28 p.i. in both the medium and low infection cohorts. No correlations between the biochemical parameters and infection intensity were observed. Peak antibody titres were reached on day 49 p.i. in the medium infection cohort and on day 42 p.i. in both the high and low infection cohorts. Infection intensity could not be correlated with the magnitude of the humoral immune response or time to seroconversion. The effect of infection intensity on time to seroconversion, magnitude and persistence of the humoral immune response was assessed. No significant differences in the titre levels between the three groups were observed. Infection intensity could not be correlated with the magnitude of the humoral response or time to seroconversion. Results of this study were in agreement with results reported in mammals (wild boars and horses) infected with other Trichinella species and showed that antibody titres could not be detected indefinitely. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2013.

Two different feeding trials were conducted to evaluate the effects of dietary supplementation with the dairy/yeast prebiotic GroBiotic-A (GBA) to Nile tilapia diets. A nutritionally complete basal diet was supplemented with GBA at either 1 or 2% of dry weight, and all three diets were fed to triplicate groups of juvenile fish in two consecutive trials. Trial 1 continued for 8 weeks, while Trial 2 was conducted for 5 weeks to more specifically assess immunological responses, intestinal characteristics and disease resistance of tilapia. At the conclusion of Trial 1, there were no differences in weight gain (WG) or feed efficiency (FE) among fish fed the three diets. However, fish fed the diet with GBA at 2% had significantly increased survival and noticeably elevated levels of plasma lysozyme compared to fish fed the basal diet or the diet with GBA at 1%. Similarly, at the conclusion of Trial 2, WG and FE were unaffected by GBA supplementation; however, fish fed the diet with GBA at 2% also exhibited elevated plasma lysozyme as well as significantly (P < 0.05) increased levels of extracellular superoxide anion production (EX-SOAP) by macrophages. Dendrogram analysis of denaturing gradient gel electrophoresis (DGGE) images detected a significantly different microbial community within the intestine of fish fed the diet with GBA at 2% compared to fish fed the basal diet and diet with GBA at 1%. None of the experimental diets resulted in significant improvements to survival after exposure to Streptococcus iniae due to within treatment variability. However, fish fed the diet with GBA at 2% did tend to experience reduced mortality (12.5%) as compared to fish fed the basal diet (35%). Thus, supplementation of GBA at 2% of diet did alter the gut microbiota of tilapia and enhanced immunological responses and disease resistance to S. iniae.

: This study assesses how South Sudan’s 2011 vote for independence has influenced the Nile Basin’s debate over water rights. Although it initially seemed that South Sudan was aligning itself with the upstream riparian states such as Ethiopia and Uganda, effectively leaving Egypt and Sudan as the only opponents to a Cooperative Framework Agreement and redefining so-called ‘historic water rights’, the escalation of the South Sudanese internal conflict between President Salva Kiir and ex-Vice-President Riek Machar changed this situation entirely. The conflict has reached a new stalemate, with Egypt giving military support to Salva Kiir in his fight against Machar, thus befriending South Sudan and strengthening its position in the Nile Basin, and Ethiopia hesitating to offer support and effectively losing South Sudan as a newly found ally. Currently, a Cooperative Framework Agreement is farther away from being signed than it was before South Sudan’s conflict escalated: South Sudan is no longer in any position to sign or implement agreements and policies regarding water issues, which allowed Egypt to reassert its dominant position in the debate. This study foresees three different possible future scenarios: one of perpetuated violent conflict, one of political conflict and one of increased interstate political cooperation.

This dissertation explores the experiences of Egyptian peasants from the Delta province of Minufiyya who were tried for murder by newly created "native" or "national" courts between 1884 and 1914. Through the study of 2,000 pages of criminal files, I deconstruct how the colonial state used the modern techniques of judicial orality, writing, and performance, both to justify a series of reforms that turned the entire legal process into a parody of justice, and to develop a grand narrative that essentialized peasants as revengeful, greedy, and passionate and ultimately linked their alleged immorality to their illiteracy. Furthermore, my work sheds light on how peasants reacted to this process of moralization of the law by promoting the "honor of the brigand" through violence and poetry. Finally, by focusing on the many petitions contained in the judicial files, my dissertation provides new insight into the development of a "vernacular" culture of the law that betrays the peasants' awareness of the highly political nature of the legal process. By presenting and analyzing an untapped wealth of Egyptian archives produced by the native courts, this research not only sheds invaluable light on the workings and hence the very nature of British colonial justice in Egypt, but also represents a significant advance in the knowledge of the origins of Egypt's current legal system. On a more theoretical level, this study also constitutes an important contribution to the reflection on the subaltern subject initiated by Rosalind O'Hanlon and Talal Asad, by showing how the peasants' agency paradoxically lies in their "disempowerment."

This dissertation explores the experiences of Egyptian peasants from the Delta province of Minufiyya who were tried for murder by newly created "native" or "national" courts between 1884 and 1914. Through the study of 2,000 pages of criminal files, I deconstruct how the colonial state used the modern techniques of judicial orality, writing, and performance, both to justify a series of reforms that turned the entire legal process into a parody of justice, and to develop a grand narrative that essentialized peasants as revengeful, greedy, and passionate and ultimately linked their alleged immorality to their illiteracy. Furthermore, my work sheds light on how peasants reacted to this process of moralization of the law by promoting the "honor of the brigand" through violence and poetry. Finally, by focusing on the many petitions contained in the judicial files, my dissertation provides new insight into the development of a "vernacular" culture of the law that betrays the peasants' awareness of the highly political nature of the legal process. By presenting and analyzing an untapped wealth of Egyptian archives produced by the native courts, this research not only sheds invaluable light on the workings and hence the very nature of British colonial justice in Egypt, but also represents a significant advance in the knowledge of the origins of Egypt's current legal system. On a more theoretical level, this study also constitutes an important contribution to the reflection on the subaltern subject initiated by Rosalind O'Hanlon and Talal Asad, by showing how the peasants' agency paradoxically lies in their "disempowerment."

The flavivirus resistance gene, Flv, in mice has been identified as 2'-5' oligoadenylate synthetase 1b (Oas1b). Susceptible mice produce a protein that is truncated (Oas1btr) at the C-terminus due to a premature stop codon encoded by a C820T transition. Mice produce 8 Oas1 proteins, Oas1a-Oas1h. In the present study, Oas1a, Oas1b and Oas1btr were expressed as MBP-fusion proteins in bacteria and purified. 2-5A synthetase activity was demonstrated using MBP-Oas1a, while neither MBP-Oas1b nor MBP-Oas1btr were functionally active. The 2-5A synthetase activity of MBP-Oas1a was inhibited in a dose-dependent manner by the addition of MBP-Oas1b but not MBPOas1btr. Finally, three RNA probes were synthesized from the 3' end of the WNV Eg101 genome and used to test the ability of the expressed Oas1 proteins to bind to viral RNA. Results of the RNA binding activity assays suggest Oas1 proteins may specifically interact with regions of WNV RNA.

The potential of the unicellular green algae Chlorella vulgaris and Scenedesmus obliquus and the filamentous green algae Cladophora glomerata and Hydrodictyon reticulatum as protein sources in Oreochromis niloticus and Tilapia zillii diets was investigated. When O. niloticus and T. zillii were fed with fresh C. vulgaris and S. obliquus, a high percentage of the ingested algae was found to be undigested. Heat treatment of the algae at 40°, 60°, 80° and 100°C produced increased growth and protein utilizations in the fishes compared to those fed the untreated algae. Feeding C. vulgaris treated at 100°C for 30 minutes and S. obliquus treated at 100°C for 15 minutes was found to have produced the best growth responses in O. niloticus and T. zillii. C. glomerata meal and H. reticulatum meal were each fed separately as fishmeal substitutes in pelleted rations formulated to contain 30% protein with varying proportions of this supplied by the fishmeal and the algal meal. A diet containing 25% protein supplied by the algal meal alone was also fed. When 5% of the fishmeal protein was replaced with algal protein (both C. glomerata and H. reticulatum) and fed to T. zillii, the growth and protein utilization values recorded were superior to those obtained for the control 30% fishmeal protein diet. Higher levels of algal protein substitution were, however, found to produce poorer growth and protein utilization values in both fish species. Diets containing only algal protein (both C. glomerata and H. reticulatum) produced the poorest growth responses in both fish species. Hydrodictyon reticulatum was found to be limiting in methionine and histidine. Supplementation of these essential amino acids produced improved growth in both O. niloticus and T. zillii. It was concluded from these studies that the green algae evaluated may be suitable partial dietary protein sources for tilapias.

Our innate immunity is our first line of defence against pathogens. We require this immunity to control the numerous viral infections we are challenged with during our lives. However, little is known about the exact molecular mechanisms of our innate immunity, particularly components that have specific antiviral potential. One potent mediator of this antiviral activity is the interferon system. Activation of the interferon system leads to the production of several interferon-induced proteins, which inhibit the multiplication of viruses by distinct mechanisms. A key example of one of these mediators is the human MxA protein. Human MxA has the capacity to inhibit many different viruses from diverse families. In many cases it is proposed that MxA interferes with key viral components, such as incoming or newly formed nucleocapsids. It is speculated that MxA traps and missorts these viral components so they are no longer available for virus production and virus dissemination is inhibited. West Nile virus belongs to Flaviviridae family of viruses and was involved in the outbreak of virus-associated encephalitis in New York City in 1999. In this thesis I show that West Nile virus is insensitive to antiviral activity of MxA and describe how West Nile virus has developed a replication strategy that avoids MxA recognition and activation. I show that virus-induced changes of cytoplasmic membranes provide a protective microenvironment for viral replication and the viral components essential for viral replication. This hypothesis was proven by preventing the formation of these membrane structures with the fungal chemical Brefeldin A. Under these conditions I observed that stable expression of MxA could partially restrict West Nile virus RNA replication. Subsequently, I showed that the assembly mechanism of West Nile virus prevents interaction between the MxA protein and the viral capsid proteins. This was achieved by the use of a trans-packaging cell line whereby the West Nile virus structural proteins are expressed stably in trans instead of in cis from the polyprotein. When this cell line was transfected with a West Nile virus replicon expressing the human MxA protein distinct co-localisation and redistribution of the MxA with West Nile virus capsid proteins into large tubular structures within the cytoplasm of transfected cells was observed. Strikingly, these tubular aggregates are visually analogous to structures observed during infection of MxA expressing cells infected with members of the Bunyaviridae, particularly La Crosse virus. Moreover, retargeting MxA to specific sites of the endoplasmic reticulum in cells transfected with the West Nile virus infectious clone resulted in co-localisation between MxA and the West Nile virus capsid proteins and significantly inhibited the production of infectious particles. These results suggest that the sequestering of viral capsids within cytoplasmic inclusions maybe a conserved mechanism for antiviral activity of the MxA protein across the viruses families and highlight the innate ability of such molecules to recognise key molecular patterns within pathogens. Finally, I sought to exploit the antiviral potential of MxA as a therapeutic agent against infection with Influenza A viruses; viruses that have a very high sensitivity for the antiviral activity of MxA. By expressing MxA from the West Nile virus replicon, infection with the highly pathogenic Influenza virus H5N1 strain could be inhibited in vitro. Furthermore, in vivo studies in Mx-negative mice indicated that intranasal inoculation with MxA expressed from the West Nile virus replicon can protect these mice against an otherwise lethal infection with a low pathogenic Influenza A virus. Taken all together, in this thesis I provide evidence that strongly supports the existence of an evolutionary working mechanism of a significant mediator of our immune system, the antiviral MxA protein. Furthermore, I show how an important human pathogen, such as West Nile virus has evolved a replication strategy to evade this antiviral protein. These results will open new pathways for the development of a new type of antiviral therapies that utilize the potent antiviral activity of the MxA protein.