Late-stage disease at presentation to an HIV clinic in eastern Tanzania: A retrospective cross-sectional study

Background Late presentation and delayed treatment initiation is associated with poor outcomes in patients with HIV. Little is known about the stage at which HIV patients present at HIV clinics in Tanzania. Aim This study aimed at determining the proportion of HIV patients presenting with WHO clinical stages 3 and 4 disease, and the level of immunity at the time of enrollment at the care and treatment center. Methods A retrospective cross-sectional study was conducted among 366 HIVinfected adults attending HIV clinic at Mwananyamala Hospital in Dar es Salaam, Tanzania. Data were obtained from the care and treatment clinic database. Results Late stage disease at the time of presentation was found in 276 (75.4%) of the patients; out of whom 153 (41.8%) presented with CD4 count <200 cells/ul and 229 (62.6%) presented with WHO clinical stage 3 or 4 at the time of clinic enrollment. Strategies to improve early diagnosis and treatment initiation should be improved.

THE PROSPECT OF BIOGAS AMONG SMALL-HOLDER DAIRY GOAT FARMERS IN THE ULUGURU MOUNTAINS, TANZANIA

Biogas can be a clean cooking alternative where biomass is the dominant source of cooking energy and where feedstock for anaerobic digestion is available. By substituting woody biomass for energy, biogas may reduce local deforestation. Tanzania has more than 15.6 million goats. Dairy goats of different breeds are found in the mid- to high altitudes of the country. Population density has made firewood increasingly scarce and there are few energy alternatives in mountainous areas such as in the Uluguru Mountains. In Mgeta ward, Morogoro region, introduction of Norwegian dairy goats in the 1980s has improved livelihoods in the area. In this study, goat manure was assessed as feedstock for biogas and as fertilizer. Field work among small-holder dairy goat farmers in Mgeta was conducted to measure daily manure production, and to provide a basic model for prediction of the quantity of droppings which may be collected by farmers. Biogas and fertilizer potential from goat manure was compared to cow and pig manure. Buswell’s formula was used to calculate approximate methane yield. The results show that goat manure from Mgeta can yield 167 l∙kg Volatile Solids-1 (VS). Compared with other substrates approximate methane yield can be ranked as pig > guatemala grass > cow > goat. The average goat of 25 kg in Mgeta leaves 61 kg Total Solids (TS) droppings per year. It was estimated that 15 goats capita-1 would be required to meet the total cooking energy needs of small-holder households in the study location. N:P:K content in goat manure (TS) is 2:1:1, similar to cow and pig manure. Goat droppings had to be macerated to reduce particle size for anaerobic digestion. Biogas from dairy goats could be combined with the year-round irrigated horticulture production in Mgeta. Vegetable gardens in the slope below the digesters could be fertilized by gravitation with the NH4+-rich bioslurry, to save labour and increase yields.

EDUCATION, TRAINING AND AWARENESS OF LAWS AS DETERMINANTS OF COMPLIANCE WITH PLANT PROTECTION LAW: THE CASE OF PESTICIDE USE PRACTICES IN TANZANIA

Pesticide residues in food and environment pose serious health risks to human beings. Plant protection laws, among other things, regulate misuse of agricultural pesticides. Compliance with such laws consequently reduces risks of pesticide residues in food and the environment. Studies were conducted to assess the compliance with plant protection laws among tomato farmers in Mvomero District, Morogoro Region, Tanzania. Compliance was assessed by examining pesticide use practices that are regulated by the Tanzanian Plant Protection Act (PPA) of 1997. A total of 91 tomato farmers were interviewed using a structured questionnaire. Purposive sampling was used in selecting at least 30 respondent farmers from each of the three villages of Msufini, Mlali and Doma in Mvomero District, Morogoro Region. Simple Random Sampling was used to obtain respondents from the sampling frame. Individual and social factors were examined on how they could affect pesticide use practices regulated by the law. Descriptive statistics, mainly frequency, were used to analyze the data while associations between variables were determined using Chi-Square and logistic regression model. The results showed that respondents were generally aware of the existence of laws on agriculture, environment and consumer health, although none of them could name a specific Act. The results revealed further that 94.5% of the farmers read instructions on the pesticides label. However, only 21% used the correct doses of pesticides, 40.7% stored pesticides in special stores, 68.1% used protective gear, while 94.5% always read instructions on the label before using a pesticide product. Training influenced the application rate of pesticide (p < 0.001) while awareness of agricultural laws significantly influenced farmers’ tendency to read information on the labels (p < 0.001). The results showed further that education significantly influenced the use of protective gears by farmers (p = 0.042). Education also significantly affected the manner in which farmers stored pesticide-applying equipment (p = 0.024). Furthermore, farmers’ awareness of environmental laws significantly (p = 0.03) affected farmers’ disposal of empty pesticide containers. Results of this study suggest the need for express provisions on safe use and handling of pesticides and related offences in the Act, and that compliance should be achieved through education rather than coercion. Results also suggest establishment of pesticide disposal mechanisms and structures to reduce unsafe disposal of pesticide containers. It is recommended that farmers should be educated and trained on proper use of pesticides. Farmers’ awareness on laws affecting food, environment and agriculture should be improved.

CLIMATE CHANGE ADAPTATION IN VULNERABLE CROP AND LIVESTOCK PRODUCTION SYSTEMS IN MGETA, TANZANIA

Increased occurrence of drought and dry spells during the growing season have resulted in increased interest in protection of tropical water catchment areas. In Mgeta, a water catchment area in the Uluguru Mountains in Tanzania, water used for vegetable and fruit production is provided through canals from the Uluguru South Forest Reserve. The clearing of forest land for cultivation in the steep slopes in the area is causing severe land degradation, which is threatening the water catchment area, livelihoods, and food security of the local communities, as well as the major population centers in the lowlands. In this paper, the economic performance of a traditional cropping-livestock system with East African (EA)-goats and pigs and extensive vegetable production is compared with a more sustainable and environmentally friendly crop-dairy goat production system. A linear programming (LP) crop-livestock model, maximizing farm income considering the environmental constraints in the area was applied for studying the economic performance of dairy goats in the production system. The model was worked out for the rainy and dry seasons and the analysis was conducted for a basic scenario representing the current situation, based on the variability in the 30 years period from 1982-2012, and in a scenario of both lower crop yields and increased crop variability due to climate change. Data obtained from a sample of 60 farmers that were interviewed using a questionnaire was used to develop and parameterize the model. The study found that in the steep slopes of the area, a crop-dairy goat system with extensive use of grass and multipurpose trees (MPTs) would do better than the traditional vegetable gardening with the EA goat production system. The crop-dairy goat system was superior both in the basic and in a climate change scenario since the yield variation of the grass and MPTs system was less affected compared to vegetable crops due to more tree cover and the use of perennial grasses. However, the goat milk production in the area was constrained by inadequate feeding and lack of an appropriate breeding program. Hence, farmers should enhance goat milk production by supplementing with more concentrate feed and by implementing goat-breeding principles. Moreover, policy measures to promote such a development are briefly discussed.

Ecologically relevant characteristics of flow-regime of Rufiji Basin in Tanzania (an ensemble of ecohydrological clues to infer associeted ramifications on dtream and ecosystem)

Dissertação de Mestrado, Ecohidrologia - Erasmus Mundus, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014

Water Demand and Allocation in the Mara River Basin, Kenya/Tanzania in the Face of Land Use Dynamics and Climate Variability

The Mara River Basin (MRB) is endowed with pristine biodiversity, socio-cultural heritage and natural resources. The purpose of my study is to develop and apply an integrated water resource allocation framework for the MRB based on the hydrological processes, water demand and economic factors. The basin was partitioned into twelve sub-basins and the rainfall runoff processes was modeled using the Soil and Water Assessment Tool (SWAT) after satisfactory Nash-Sutcliff efficiency of 0.68 for calibration and 0.43 for validation at Mara Mines station. The impact and uncertainty of climate change on the hydrology of the MRB was assessed using SWAT and three scenarios of statistically downscaled outputs from twenty Global Circulation Models. Results predicted the wet season getting more wet and the dry season getting drier, with a general increasing trend of annual rainfall through 2050. Three blocks of water demand (environmental, normal and flood) were estimated from consumptive water use by human, wildlife, livestock, tourism, irrigation and industry. Water demand projections suggest human consumption is expected to surpass irrigation as the highest water demand sector by 2030. Monthly volume of water was estimated in three blocks of current minimum reliability, reserve (>95%), normal (80–95%) and flood (40%) for more than 5 months in a year. The assessment of water price and marginal productivity showed that current water use hardly responds to a change in price or productivity of water. Finally, a water allocation model was developed and applied to investigate the optimum monthly allocation among sectors and sub-basins by maximizing the use value and hydrological reliability of water. Model results demonstrated that the status on reserve and normal volumes can be improved to ‘low’ or ‘moderate’ by updating the existing reliability to meet prevailing demand. Flow volumes and rates for four scenarios of reliability were presented. Results showed that the water allocation framework can be used as comprehensive tool in the management of MRB, and possibly be extended similar watersheds.

Corporate social responsibility reporting in the mining sector of Tanzania:(Lack of) government regulatory controls and NGO activism

Purpose – The purpose of this paper is to contribute to the ongoing debate on governance, accountability, transparency and corporate social responsibility (CSR) in the mining sector of a developing country context. It examines the reporting practices of the two largest transnational gold-mining companies in Tanzania in order to draw attention to the role played by local government regulations and advocacy and campaigning by nationally organised non-governmental organisations (NGOs) with respect to promoting corporate social reporting practices. Design/methodology/approach – The paper takes a political economy perspective to consider the serious implications of the neo-liberal ideologies of the global capitalist economy, as manifested in Tanzania’s regulatory framework and in NGO activism, for the corporate disclosure, accountability and responsibility of transnational companies (TNCs). A qualitative field case study methodology is adopted to locate the largely unfamiliar issues of CSR in the Tanzanian mining sector within a more familiar literature on social accounting. Data for the case study were obtained from interviews and from analysis of documents such as annual reports, social responsibility reports, newspapers, NGO reports and other publicly available documents. Findings – Analysis of interviews, press clips and NGO reports draws attention to social and environmental problems in the Tanzanian mining sector, which are arguably linked to the manifestation of the broader crisis of neo-liberal agendas. While these issues have serious impacts on local populations in the mining areas, they often remain invisible in mining companies’ social disclosures. Increasing evidence of social and environmental ills raises serious questions about the effectiveness of the regulatory frameworks, as well as the roles played by NGOs and other pressure groups in Tanzania. Practical implications – By empowering local NGOs through educational, capacity building, technological and other support, NGOs’ advocacy, campaigning and networking with other civil society groups can play a pivotal role in encouraging corporations, especially TNCs, to adopt more socially and environmentally responsible business practices and to adhere to international and local standards, which in turn may help to improve the lives of many poor people living in developing countries in general, and Tanzania in particular. Originality/value – This paper contributes insights from gold-mining activities in Tanzania to the existing literature on CSR in the mining sector. It also contributes to political economy theory by locating CSR reporting within the socio-political and regulatory context in which mining operations take place in Tanzania. It is argued that, for CSR reporting to be effective, robust regulations and enforcement and stronger political pressure must be put in place.

Analys av ett mikronät vid Ihushi Development Center i Tanzania

Denna studie omfattar en undersökning om hur ett hybridnät har fungerat, i detta fall Ihushi Development Center som ligger I Tanzania. De mätningar som har gjorts, har följt en standard för att kunna universellt användas vid en fortsatt studie eller direkt kunna användas för att jämföras med andra hybridnät med liknande uppsättning och förutsättningar. Under arbetets gång så har en ny modell tagits fram för att smidigt kunna analysera rådata och uträkning av de nödvändiga parametrarna. Detta underlättar även kommande arbeten kring detta hybridnät. Det har också blivit en typ av simulering då det har funnits många olika typer av utspridda och kontinuerliga fel som har behövts hanteras. Dessa värden har då behövts uppskattats utifrån olika källor och metoder, för att sedan användas. Det har sedan räknats ut effektiviteter och prestanda på olika delar i systemet som sedan kommenteras och kan direkt användas för en utvärdering i en framtida studie. Dessa resultat har bitvis jämförts med tidigare utvärdering men då det saknats information från föregående rapport så har en fullständig jämförelse och slutsats inte varit möjlig.

The epidemiology of foot-and-mouth disease at the wildlife-livestock interface in northern Tanzania

Foot-and-mouth disease (FMD), a disease of cloven hooved animals caused by FMD virus (FMDV), is one of the most economically devastating diseases of livestock worldwide. The global burden of disease is borne largely by livestock-keepers in areas of Africa and Asia where the disease is endemic and where many people rely on livestock for their livelihoods and food-security. Yet, there are many gaps in our knowledge of the drivers of FMDV circulation in these settings. In East Africa, FMD epidemiology is complicated by the circulation of multiple FMDV serotypes (distinct antigenic variants) and by the presence of large populations of susceptible wildlife and domestic livestock. The African buffalo (Syncerus caffer) is the only wildlife species with consistent evidence of high levels of FMDV infection, and East Africa contains the largest population of this species globally. To inform FMD control in this region, key questions relate to heterogeneities in FMD prevalence and impacts in different livestock management systems and to the role of wildlife as a potential source of FMDV for livestock. To develop FMD control strategies and make best use of vaccine control options, serotype-specific patterns of circulation need to be characterised. In this study, the impacts and epidemiology of FMD were investigated across a range of traditional livestock-keeping systems in northern Tanzania, including pastoralist, agro-pastoralist and rural smallholder systems. Data were generated through field studies and laboratory analyses between 2010 and 2015. The study involved analysis of existing household survey data and generated serological data from cross-sectional livestock and buffalo samples and longitudinal cattle samples. Serological analyses included non-structural protein ELISAs, serotype-specific solid-phase competitive ELISAs, with optimisation to detect East African FMDV variants, and virus neutralisation testing. Risk factors for FMDV infection and outbreaks were investigated through analysis of cross-sectional serological data in conjunction with a case-control outbreak analysis. A novel Bayesian modeling approach was developed to infer serotype-specific infection history from serological data, and combined with virus isolation data from FMD outbreaks to characterise temporal and spatial patterns of serotype-specific infection. A high seroprevalence of FMD was detected in both northern Tanzanian livestock (69%, [66.5 - 71.4%] in cattle and 48.5%, [45.7-51.3%] in small ruminants) and in buffalo (80.9%, [74.7-86.1%]). Four different serotypes of FMDV (A, O, SAT1 and SAT2) were isolated from livestock. Up to three outbreaks per year were reported by households and active surveillance highlighted up to four serial outbreaks in the same herds within three years. Agro-pastoral and pastoral livestock keepers reported more frequent FMD outbreaks compared to smallholders. Households in all three management systems reported that FMD outbreaks caused significant impacts on milk production and sales, and on animals’ draught power, hence on crop production, with implications for food security and livelihoods. Risk factor analyses showed that older livestock were more likely to be seropositive for FMD (Odds Ratio [OR] 1.4 [1.4-1.5] per extra year) and that cattle (OR 3.3 [2.7-4.0]) were more likely than sheep and goats to be seropositive. Livestock managed by agro-pastoralists (OR 8.1 [2.8-23.6]) or pastoralists (OR 7.1 [2.9-17.6]) were more likely to be seropositive compared to those managed by smallholders. Larger herds (OR: 1.02 [1.01-1.03] per extra bovine) and those that recently acquired new livestock (OR: 5.57 [1.01 – 30.91]) had increased odds of suffering an FMD outbreak. Measures of potential contact with buffalo or with other FMD susceptible wildlife did not increase the likelihood of FMD in livestock in either the cross-sectional serological analysis or case-control outbreak analysis. The Bayesian model was validated to correctly infer from ELISA data the most recent serotype to infect cattle. Consistent with the lack of risk factors related to wildlife contact, temporal and spatial patterns of exposure to specific FMDV serotypes were not tightly linked in cattle and buffalo. In cattle, four serial waves of different FMDV serotypes that swept through southern Kenyan and northern Tanzanian livestock populations over a four-year period dominated infection patterns. In contrast, only two serotypes (SAT1 and SAT2) dominated in buffalo populations. Key conclusions are that FMD has a substantial impact in traditional livestock systems in East Africa. Wildlife does not currently appear to act as an important source of FMDV for East African livestock, and control efforts in the region should initially focus on livestock management and vaccination strategies. A novel modeling approach greatly facilitated the interpretation of serological data and may be a potent epidemiological tool in the African setting. There was a clear temporal pattern of FMDV antigenic dominance across northern Tanzania and southern Kenya. Longer-term research to investigate whether serotype-specific FMDV sweeps are truly predictable, and to shed light on FMD post-infection immunity in animals exposed to serial FMD infections is warranted.

The impact and control of malignant catarrhal fever in Tanzania

Malignant Catarrhal Fever (MCF), an often-lethal infectious disease, presents as a variable complex of lesions in susceptible ungulate species. The disease is caused by a -herpesvirus following transmission from an inapparent carrier host. Two major epidemiological forms exist: wildebeest-associated MCF (WA-MCF), in which the virus is transmitted to susceptible species by wildebeest calves less than approximately four months of age, and sheepassociated MCF (SA-MCF) in which the virus is spread by sheep (primarily adolescents). Due to the lack of an in-vitro propagation system for the causative agent of the more economically significant SA-MCF, and with the expectation that cross-protective immunity may be provided, vaccine development has focused on the more easily propagated alcelaphine herpesvirus-1 (AlHV-1) that causes WA-MCF. In 2008 a direct viral challenge trial showed that a novel vaccine, employing an attenuated AlHV-1 (atAlHV-1) `C5000 virus strain, protected British Friesian-Holstein (FH) cattle against an intranasal challenge with virulent AlHV-1 `C5000 virus. For cattle keeping people living near wildebeest calving areas in sub-Saharan Africa an effective vaccine would have value as it would release them from the costly annual disease avoidance strategy of having to move their herds away from the oncoming wildebeest. On the other hand, an effective vaccine will release herd owners from the need to avoid MCF, allowing them to graze their cattle alongside wildebeest on the highly nutritious pastures of the calving areas. As such conservationists have raised concerns that the development of a vaccine might lead to detrimental grazing competition. The principle objective of this study was to test the novel vaccine on Tanzanian shorthorn zebu cross cattle (SZC).We did this firstly using a natural challenge field trial (Chapter Two) which demonstrated that immunisation with the atAlHV-1 vaccine was well tolerated and induced an oro-nasopharyngeal AlHV-1-specific and -neutralising antibody response. This resulted in an immunity in SZC cattle that was partially protective and reduced naturally transmitted infection by 56%. We also demonstrated that non-fatal infections occurred with a much higher frequency than previously thought. Because the calculated efficacy of the vaccine was less than that seen in British FH cattle we wanted to determine whether host factors, particular to SZC cattle, had impacted the outcomes of the field trial. To do this we repeated the 2008 direct viral challenge trial using SZC cattle (Chapter Four). During this trial we also investigated whether the recombinant bacterial flagellin monomer (FliC), when used as an adjuvant, might improve the vaccine’s efficacy. The findings from this trial indicated that direct challenge with pathogenic AlHV-1 is effective at inducing MCF in SZC cattle and that FliC is not an appropriate adjuvant for this vaccine. Furthermore, with less control group cattle dying of MCF than expected we speculate that SZC cattle may have a degree of resistance to MCF that affords them protection from infection and developing fatal disease. In Chapter Three we investigated aspects of the epidemiology of MCF, specifically whether wildebeest placenta, long implicated by Maasai cattle owners as a source of MCF, might play a role in viral transmission. Additionally, through comparative sequence analysis, at two specific genes (A9.5 and ORF50) of wild-type and atAlHV-1, we investigated whether the `C5000 strain, the source of which was taken from Africa more than 40 years ago, was appropriate for vaccine development. The detection of AlHV-1 virus in approximately 50% of placentae indicated that infection can occur in-utero and that this tissue might play a role in disease transmission. And, despite describing three new alleles of the A9.5 gene (supporting previous evidence that this gene is polymorphic and encodes a secretory protein with interleukin-4 as the major homologue), the observation that the most frequently detected haplotypes, in both wild-type and attenuated AlHV-1, were identical suggests that AlHV-1 has a slow molecular clock and that the attenuated strain was appropriate for vaccine development. In Chapter Five we present the first quantitative assessment of the annual MCF avoidance costs that Maasai pastoralists incur. In particular we estimated that as a result of MCF avoidance 64% of the total daily milk yield during the MCF season was not available to be used by the 81% of the family unit remaining at the permanent boma. This represents an upper-bound loss of approximately 8% of a household0s annual income. Despite these considerable losses we concluded that, given an incidence of fatal MCF in cattle living in wildebeest calving areas of 5% to 10%, if herd owners were to stop trying to avoid MCF by allowing their cattle to graze alongside wildebeest, any gains made through increased availability of milk, improved body condition and reduced energy demands would be offset by an increase in MCF-incidence. With the development of an effective vaccine, however, this alternative strategy might become optimal. The overall conclusion we draw therefore is that, despite the substantial costs incurred each year avoiding MCF, the partial protection afforded by the novel vaccine strategy is not sufficient to warrant a wholesale change in disease avoidance strategy. Nonetheless, even the partial protection provided by this vaccine could be of value to protect animals that cannot be moved, for example where some of the herd remain at the boma to provide milk or where land-use changes make traditional disease avoidance difficult. Furthermore, the vaccine may offer a feasible solution to some of the current land-use challenges and conflicts, providing a degree of protection to valuable livestock where avoidance strategies are not possible, but with less risk of precipitating the potentially damaging environmental consequences, such as overgrazing of highly nutritious seasonal pastures, that might result if herd owners decide they no longer need to avoid wildebeest.

Rural Poultry in the Developing world

In 2007 I travelled to Mozambique and Tanzania to photographically document the work undertaken by a group of Australians who are working to bring a self sufficient lifestyle back to the HIV Aids stricken communities of Africa. University of Queensland veterinary researchers have developed a vaccination that can eradicate disease from local rural poultry. The Kyeema Foundation is working in country to supply this vaccine to families battling HIV AIDS and to teach local residents how to successfully implement it. QUT, AusAID and the Kyeema Foundation funded the trip.

African Burkitt Lymphoma: Age-Specific Risk and Correlations with Malaria Biomarkers

African Burkitt lymphoma is an aggressive B-cell, non-Hodgkin lymphoma linked to Plasmodium falciparum malaria. Malaria biomarkers related to onset of African Burkitt lymphoma are unknown. We correlated age-specific patterns of 2,602 cases of African Burkitt lymphoma (60% male, mean ± SD age = 7.1 ± 2.9 years) from Uganda, Ghana, and Tanzania with malaria biomarkers published from these countries. Age-specific patterns of this disease and mean multiplicity of P. falciparum malaria parasites, defined as the average number of distinct genotypes per positive blood sample based on the merozoite surface protein-2 assessed by polymerase chain reaction, were correlated and both peaked between 5 and 9 years. This pattern, which was strong and consistent across regions, contrasted parasite prevalence, which peaked at 2 years and decreased slightly, and geometric mean parasite density, which peaked between 2 and 3 years and decreased sharply. Our findings suggest that concurrent infection with multiple malaria genotypes may be related to onset of African Burkitt lymphoma.

H. pylori-infection and antibody immune response in a rural Tanzanian population

Abstract Background: Helicobacter pylori (H. pylori) infection is ubiquitous in sub-Saharan Africa, but paradoxically gastric cancer is rare. Methods: Sera collected during a household-based survey in rural Tanzania in 1985 were tested for anti-H. pylori IgG and IgG subclass antibodies by enzyme immunoassay. Odds ratios (OR) and confidence intervals (CI) of association of seropositivity with demographic variables were computed by logistic regression models. Results: Of 788 participants, 513 were aged ≤17 years. H. pylori seropositivity increased from 76% at 0–4 years to 99% by ≥18 years of age. Seropositivity was associated with age (OR 11.5, 95% CI 4.2–31.4 for 10–17 vs. 0–4 years), higher birth-order (11.1; 3.6–34.1 for ≥3rd vs. 1st born), and having a seropositive next-older sibling (2.7; 0.9–8.3). Median values of IgG subclass were 7.2 for IgG1 and 2.0 for IgG2. The median IgG1/IgG2 ratio was 3.1 (IQR: 1.7–5.6), consistent with a Th2- dominant immune profile. Th2-dominant response was more frequent in children than adults (OR 2.4, 95% CI 1.3–4.4). Conclusion: H. pylori seropositivity was highly prevalent in Tanzania and the immunological response was Th2-dominant. Th2-dominant immune response, possibly caused by concurrent bacterial or parasitic infections, could explain, in part, the lower risk of H. pylori-associated gastric cancer in Africa.

Viruses of banana in East Africa

Bananas are one of the world's most important food crops, providing sustenance and income for millions of people in developing countries and supporting large export industries. Viruses are considered major constraints to banana production, germplasm multiplication and exchange, and to genetic improvement of banana through traditional breeding. In Africa, the two most important virus diseases are bunchy top, caused by Banana bunchy top virus (BBTV), and banana streak disease, caused by Banana streak virus (BSV). BBTV is a serious production constraint in a number of countries within/bordering East Africa, such as Burundi, Democratic Republic of Congo, Malawi, Mozambique, Rwanda and Zambia, but is not present in Kenya, Tanzania and Uganda. Additionally, epidemics of banana streak disease are occurring in Kenya and Uganda. The rapidly growing tissue culture (TC) industry within East Africa, aiming to provide planting material to banana farmers, has stimulated discussion about the need for virus indexing to certify planting material as virus-free. Diagnostic methods for BBTV and BSV have been reported and, for BBTV, PCR-based assays are reliable and relatively straightforward. However for BSV, high levels of serological and genetic variability and the presence of endogenous virus sequences within the banana genome complicate diagnosis. Uganda has been shown to contain the greatest diversity in BSV isolates found anywhere in the world. A broad-spectrum diagnostic test for BSV detection, which can discriminate between endogenous and episomal BSV sequences, is a priority. This PhD project aimed to establish diagnostic methods for banana viruses, with a particular focus on the development of novel methods for BSV detection, and to use these diagnostic methods for the detection and characterisation of banana viruses in East Africa. A novel rolling-circle amplification (RCA) method was developed for the detection of BSV. Using samples of Banana streak MY virus (BSMYV) and Banana streak OL virus (BSOLV) from Australia, this method was shown to distinguish between endogenous and episomal BSV sequences in banana plants. The RCA assay was used to screen a collection of 56 banana samples from south-west Uganda for BSV. RCA detected at least five distinct BSV isolates in these samples, including BSOLV and Banana streak GF virus (BSGFV) as well as three BSV isolates (Banana streak Uganda-I, -L and -M virus) for which only partial sequences had been previously reported. These latter three BSV had only been detected using immuno-capture (IC)-PCR and thus were possible endogenous sequences. In addition to its ability to detect BSV, the RCA protocol was also demonstrated to detect other viruses within the family Caulimoviridae, including Sugar cane bacilliform virus, and Cauliflower mosaic virus. Using the novel RCA method, three distinct BSV isolates from both Kenya and Uganda were identified and characterised. The complete genome of these isolates was sequenced and annotated. All six isolates were shown to have a characteristic badnavirus genome organisation with three open reading frames (ORFs) and the large polyprotein encoded by ORF 3 was shown to contain conserved amino acid motifs for movement, aspartic protease, reverse transcriptase and ribonuclease H activities. As well, several sequences important for expression and replication of the virus genome were identified including the conserved tRNAmet primer binding site present in the intergenic region of all badnaviruses. Based on the International Committee on Taxonomy of Viruses (ICTV) guidelines for species demarcation in the genus Badnavirus, these six isolates were proposed as distinct species, and named Banana streak UA virus (BSUAV), Banana streak UI virus (BSUIV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), Banana streak CA virus (BSCAV) and Banana streak IM virus (BSIMV). Using PCR with species-specific primers designed to each isolate, a genotypically diverse collection of 12 virus-free banana cultivars were tested for the presence of endogenous sequences. For five of the BSV no amplification was observed in any cultivar tested, while for BSIMV, four positive samples were identified in cultivars with a B-genome component. During field visits to Kenya, Tanzania and Uganda, 143 samples were collected and assayed for BSV. PCR using nine sets of species-specific primers, and RCA, were compared for BSV detection. For five BSV species with no known endogenous counterpart (namely BSCAV, BSUAV, BSUIV, BSULV and BSUMV), PCR was used to detect 30 infections from the 143 samples. Using RCA, 96.4% of these samples were considered positive, with one additional sample detected using RCA which was not positive using PCR. For these five BSV, PCR and RCA were both useful for identifying infected samples, irrespective of the host cultivar genotype (Musa A- or B-genome components). For four additional BSV with known endogenous counterparts in the M. balbisiana genome (BSOLV, BSGFV, BSMYV and BSIMV), PCR was shown to detect 75 infections from the 143 samples. In 30 samples from cultivars with an A-only genome component there was 96.3% agreement between PCR positive samples and detection using RCA, again demonstrating either PCR or RCA are suitable methods for detection. However, in 45 samples from cultivars with some B-genome component, the level of agreement between PCR positive samples and RCA positive samples was 70.5%. This suggests that, in cultivars with some B-genome component, many infections were detected using PCR which were the result of amplification of endogenous sequences. In these latter cases, RCA or another method which discriminates between endogenous and episomal sequences, such as immuno-capture PCR, is needed to diagnose episomal BSV infection. Field visits were made to Malawi and Rwanda to collect local isolates of BBTV for validation of a PCR-based diagnostic assay. The presence of BBTV in samples of bananas with bunchy top disease was confirmed in 28 out of 39 samples from Malawi and all nine samples collected in Rwanda, using PCR and RCA. For three isolates, one from Malawi and two from Rwanda, the complete nucleotide sequences were determined and shown to have a similar genome organisation to previously published BBTV isolates. The two isolates from Rwanda had at least 98.1% nucleotide sequence identity between each of the six DNA components, while the similarity between isolates from Rwanda and Malawi was between 96.2% and 99.4% depending on the DNA component. At the amino acid level, similarities in the putative proteins encoded by DNA-R, -S, -M, - C and -N were found to range between 98.8% to 100%. In a phylogenetic analysis, the three East African isolates clustered together within the South Pacific subgroup of BBTV isolates. Nucleotide sequence comparison to isolates of BBTV from outside Africa identified India as the possible origin of East African isolates of BBTV.

Integrating Intangible Cultural Heritage elements and learning strategy : a case study

Tanzania has a rich and diverse cultural history based on community cultural life. However, at present, young people have limited opportunity to exploit this richness of creative expressions and engage in creative jobs as their future career. Hence, the significant challenge remains: how to integrate Intangible cultural heritage elements and learning strategy as a means of promoting creative jobs for youth. This paper presents a case study on 'Strategies for youth employment in Tanzania: A creative industries approach'. The case study employed mixed methods incorporating questionnaires, interviews and focus groups and was held in Dar-Es-Salaam, Mwanza, Dodoma, Lindi and Morogoro from July to October, 2012. This paper discusses some of the issues and argues that there is no virtual utilization of the intangible cultural heritage knowledge and skills in 'putting education to work' (UNESCO, 2012) for the better prospects of youth. Although the discussion is specific to Tanzania, the case may also apply to other developing countries.