Identification and characterisation of an extrachromosomal element from a multidrug-resistant isolate of Trypanosoma brucei brucei

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Drug resistance together with difficulties involved in the development of new trypanocides are a major problem in the present control of African trypanosomiasis. DNA based diagnostics for drug resistance would overcome problems in the identification of drug-resistant populations and contribute to effective control measures. However, this requires a detailed knowledge of the mode of action and the mechanisms by which trypanosomes can overcome the toxic effects of trypanocides. In this study, a search for molecular differences between a multidrug-resistant isolate of Trypanosoma brucei brucei, CP 547, and a reference drug-sensitive population, ILTat 1.4, led to the identification of a 6.6 kbp extrachromosomal element in the multidrug-resistant population. In light of the involvement of extrachromosomal elements in drug resistance in Leishmana spp. and cancer cells, the identification of the 6.6 kbp element warranted its characterisation. Several different approaches sere attempted before a sequence which hybridised to the 6.6 kbp element its eventually isolated. This sequence is represented by a 108 bp repeat sequence which forms long arrays of tandem repeats. Since N/a III is the sole restriction enzyme that cuts within the repeat, it has been referred to as an N/a III repeal The repeat is flanked by a 5 bp spacer sequence. However, a unique 5 bp direct repeat flanking two complete, and one partial copy of the N/a III repeat may signify the transposition of these sequences. Hybridisation with the N/a III repeat revealed the presence of 'higher' hybridising elements which also appear to be predominantly composed of long tandem arrays of the N/a Ill repeal Through exploitation of the p01) merase chain reaction using arbitrary primers (AP-PCR), additional sequences were identified which are associated with some of the 6.6 kbp and 'higher' hybridising elements. The 6.6 kbp element and some of the 'higher' hybridising elements display features of circular DNA molecules. The 6.6 kbp element also displays some level of size and sequence heterogeneity within different populations of the same trypanosome isolate. The copy number of the 6.6 kbp element is also not stable and appears to be directly affected by the application of selective drug pressure, but a direct association between the presence of the element and the expression of multidrug resistance could not be determined. The N/a III repeat family represents a newly identified repetitive family specific to members of the Trypanozoon subgenus. This repeat family, representing about 5% of the parasite genome, is dispersed through all size classes of chromosomes, in addition to its presence on the extrachromosomal elements. Transcriptional studies of the N/a III repeats have revealed that their transcription is developmentally regulated, since heterogeneous transcripts ranging from greater than 10 kb to smaller than 300 bp are present in the actively dividing long slender bloodstream and insect stage procyclic forms of the parasite but not nondividing, stumpy bloodstream forms. Lastly, the N/a III repeat lacks an open reading frame and transcripts do not appear to have a spliced leader sequence at the 5' end. Furthermore, there is almost an equal representation of polyadenylatcd and non-polyadenlyated transcripts

Women and men in tropical dry forests: a preliminary review

From a broad review of 670 publications on gender and forests, ~130 were found to address the world’s dry forests. These were examined with the intent to extract gendered social, cultural, political and economic patterns of relevance in such forests. Seven interrelated themes recurred in this literature: 1) population pressure, 2) migration, 3) intra-familial and inter-group conflict, 4) hierarchy and significant power differences, 5) strict gender differentiation, 6) commercialization of crops and NTFPs, and 7) fuelwood collection. Based upon these themes, the uniqueness of each situation and the importance of finetuning any approach to local realities to generate outcomes that can benefit women, we propose four promising ways to enhance the prospects for gender equity in dry forest areas: 1) a strengthening of groups and collective action, 2) explicit challenges to traditional gender norms, 3) a focus on products and spaces that interest women, and 4) addressing migration and population issues

A simple field based method for rapid wood density estimation for selected tree species in Western Kenya

Wood density is an important variable for accurate quantification of woody biomass and carbon stocks. Conventional destructive methods for wood density estimation are resource intensive, prohibiting their use, limiting the application of approaches that would minimize uncertainties in tree biomass estimates. We tested an alternative method involving tree coring with a carpenter's auger to estimate wood density of seven tropical tree species in Western Kenya. We used conventional water immersion method to validate results from the auger core method. The mean densities (and 95% confidence intervals) ranged from 0.36 g cm−3 (0.25–0.47) to 0.67 g cm−3 (0.61–0.73) for the auger core method, and 0.46 g cm−3 (0.42–0.50) to 0.67 g cm−3 (0.61–0.73) for the water immersion method. The auger core and water immersion methods were not significantly different for four out of seven tree species namely; Acacia mearnsii, Mangifera indica, Eucalyptus grandis and Grevillea robusta. However, wood densities estimated from the auger core method were lower (t (61) = 7.992, P = <0.001). The ease of the auger core method application, as a non-destructive method in acquiring wood density data, is a worthy alternative in biomass and carbon stocks quantification. This method could protect trees outside forests found in most parts of Africa

Boswellia and Commiphora Species as a Resource Base for Rural Livelihood Security in the Horn of Africa: A Systematic Review

The dryland vegetation and particularly the Acacia-Commiphora woodlands support the livelihoods of approximately 52 million rural households in the Horn of Africa. Aromatic resins are valuable non-wood forest products (NWFPs) derived from Boswellia and Commiphora species in the drylands of this region. The study seeks to answer the following main questions: “What are the ecological and livelihood roles of resin producing species, and the role that people have in either degrading or restoring these ecosystems?” “Who are the participants in frankincense and myrrh production, processing, and trade, and how do these people interact?” “What is the current and potential future economic impact of frankincense and myrrh production and trade at the household level?” “What are the barriers to enhanced economic outcomes?” The study involves the use of PRISMA method—a systematic methodology to identify, select and analyze the recent literature on aromatic resins in relation to such factors as socio-economic situation, livelihood security, value chain, climate change adaptation, ecology and sustainable development in the Horn of Africa. Systematic identification of publications was conducted using several sources, including but not limited to electronic databases for literature search. Web of Science, Social Science Citation Index and Google Scholar and various scientific journals were investigated using search terms and restrictions. A total of 991 references were retrieved, but literature only published between 2003 to 2017 was selected, which led to the use of 51 works for full-text assessment. The results indicate that of the 51 selected studies, 45% focused on ecology and sustainable management, 31% on economic contribution and livelihood security, 20% on production and value chain development, and 4% on climate change adaptation and mitigation. It could be concluded that farmers’ adoption of Boswellia and Commiphora species as economic tree crops in the Horn of Africa has a distinct role in biodiversity conservation and climate change adaptation by contributing to the sustainability of ecosystem functioning as well as improving household incomes and the rural livelihood security in general, and thereby facilitating poverty alleviation

Boswellia and Commiphora Species as a Resource Base for Rural Livelihood Security in the Horn of Africa: A Systematic Review

The dryland vegetation and particularly the Acacia-Commiphora woodlands support the livelihoods of approximately 52 million rural households in the Horn of Africa. Aromatic resins are valuable non-wood forest products (NWFPs) derived from Boswellia and Commiphora species in the drylands of this region. The study seeks to answer the following main questions: “What are the ecological and livelihood roles of resin producing species, and the role that people have in either degrading or restoring these ecosystems?” “Who are the participants in frankincense and myrrh production, processing, and trade, and how do these people interact?” “What is the current and potential future economic impact of frankincense and myrrh production and trade at the household level?” “What are the barriers to enhanced economic outcomes?” The study involves the use of PRISMA method—a systematic methodology to identify, select and analyze the recent literature on aromatic resins in relation to such factors as socio-economic situation, livelihood security, value chain, climate change adaptation, ecology and sustainable development in the Horn of Africa. Systematic identification of publications was conducted using several sources, including but not limited to electronic databases for literature search. Web of Science, Social Science Citation Index and Google Scholar and various scientific journals were investigated using search terms and restrictions. A total of 991 references were retrieved, but literature only published between 2003 to 2017 was selected, which led to the use of 51 works for full-text assessment. The results indicate that of the 51 selected studies, 45% focused on ecology and sustainable management, 31% on economic contribution and livelihood security, 20% on production and value chain development, and 4% on climate change adaptation and mitigation. It could be concluded that farmers’ adoption of Boswellia and Commiphora species as economic tree crops in the Horn of Africa has a distinct role in biodiversity conservation and climate change adaptation by contributing to the sustainability of ecosystem functioning as well as improving household incomes and the rural livelihood security in general, and thereby facilitating poverty alleviation

Introduction from the Wild and Growth Characterization of Three Provenances of Calotropis procera (Ait) in a Domesticated State in Dry lands of South Eastern Kenya

Calotropis procera is a wild species that is drought-resistant and important in production of wool, fibre, biomass among other uses. There exist high demand of the wool in Asian countries and collection from the wild has been going on in Kenya and other countries. However, this collection does not meet the quantity required. Domestication of the species may be the key in bridging the quality and quantity demands for the wool. A study is being undertaken to evaluate growth, phenology and wool productivity of selected provenances of C. procera in dry lands of S. Eastern Kenya. The research site is situated between 01.313580S, 037.755460 E and 01.314220S, 037.755760E and elevation of 1173m a.s.l in South Eastern Kenya University (SEKU), Kitui County, Kenya. The research started in January 2015 with the main focus on monitoring the growth, phenological characteristics and wool productivity of the species in a typical farm setting. This paper focuses on growth characterization of three provenances of C. procera under different spacings (1.5mx1.5m, 2mx2m and 3mx3m). Results indicate that the species can be domesticated, it is hardy and capable of achieving an average field survival of over 97%. The species is multi-stemmed with Tharaka provenance showing highest mean branching of 13.25 followed by Baringo (12.22) then Kibwezi (11.98). Kibwezi recorded a slightly higher DBH growth of 3.90cm followed by Baringo (3.83) then Tharaka (3.82). Tharaka had highest mean height of 187.89cm, Baringo (184.25) and Kibwezi (182.63). Test of homogeneity of variances showed significant statistical differences (P&lt;0.5) with Kibwezi being the least significant (0.043), Baringo (0.01) and Tharaka (0.000). All provenances showed a strong positive correlation (Pearson, P&lt;0.01, n = 12) of branching, DBH and Height with Kibwezi recording rs = 0.975, Baringo (rs = 0.988) and Tharaka (rs = 0.996). Differences in spacing levels started affecting growth parameters from the age of ten months with 3x3 showing highest DBH followed by 2x2 then 1.5x1.5. In terms of height, 1.5x1.5 has the highest (182.85cm), 2x2 (172.42) and 3x3 (168.65). 3x3 was not statistically significant (0.806, P&lt;0.05) while 2x2 and 1.5x1.5 had significance of 0.001 and 0.000 respectively. All spacing levels showed strong positive correlations (Spearman, P&lt;0.01, n = 12) of the study parameters where 1.5x1.5 had rs = 0.614, 2x2 (rs = 0.972) and 3x3 (rs = 0.986) all at P&lt;0.01. The study can authoritatively conclude that the species can establish and grow well in a typical farm setting in dry lands. Spacing affects growth parameters from the age of 10 months. Baringo provenance and 2x2 spacing have performed best. The study recommends analysis of wool productivity to justify the best provenance and spacing. Keywords: Calotropis procera, Domestication, Kibwezi Provenance, Tharaka Provenance, Baringo provenanc

The management of tree genetic resources and the livelihoods of rural communities in the tropics: non-timber forest products, smallholder agroforestry practices and tree commodity crops

Products and services provided by trees in forests and farmland support the needs and promote the wellbeing of hundreds of millions of people in the tropics. Value depends on managing both the diversity of tree species present in landscapes and the genetic variation within these species. The benefits from trees and their genetic resources are, however, often not well quantified because trade is frequently outside formal markets, there is a multiplicity of species and ways in which trees are used and managed, and genetic diversity within species is frequently not given proper consideration. We review here what is known about the value of trees to rural communities through considering three production categories: non-timber products harvested from trees in natural and managed forests and woodlands; the various products and services obtained from a wide range of trees planted and/or retained in smallholders’ agroforestry systems; and the commercial products harvested from cultivated tree commodity crops. Where possible, we focus on the role of intra-specific genetic variation in providing support to livelihoods, and for each of the three production categories we also consider wider conservation and sustainability issues, including the linkages between categories in terms of management. Challenges to ‘conventional wisdom’ on tree resource use, value and management – such as in the posited links between commercialisation, cultivation and conservation – are highlighted, and constraints and opportunities to maintain and enhance value are described