Molecular characterization of the Arabidopsis thaliana - Botrytis cinerea interaction

Includes bibliographical references (leaves 199-253).This study attempted to characterize at a transcriptional level, the defence responses of Arabidopsis thaliana after infection by Botrytis cinerea, using microarrays. The first microarray experiment focused on profiling Arabidopsis genes induced by B. cinerea over time (temporal) while the second investigated spatial expression of Arabidopsis genes from the point of inoculation. A number of genes were up- and down-regulated specifically at 12 hrs, others at 24 hrs while others were up- and down-regulated at both time points. Similarly, some genes were specifically induced very close to the lesion while others in more distal tissue

Reaching for the low hanging fruits : one health benefits of joint crop-livestock services for small-scale farmers

The benefits of joint health service delivery remain under-explored in One Health. Plant clinics are known to provide; ad hoc; , undocumented advice on animal health and production to farmers. To understand the scope of this activity, 180 plant doctors (extension workers) in Uganda, Kenya, Zambia, Peru and Costa Rica were surveyed and a workshop involving key stakeholders was organized in Uganda. Most (81%) plant doctors regularly received queries from farmers on livestock topics. This shows that the single sectoral approach to service delivery often does not match small-scale farmers' needs. There is growing interest among service providers, ministry officials and researchers to improve integration of farmer services to reduce operational costs and make better use of existing capacities. The workshop supported the proposal for the first 'crop-livestock clinics' to be trialled and evaluated in Uganda. This will inform other countries on the potential of joint services to mixed crop-livestock farming communities

Rural livelihood diversity and its influence on the ecological intensification potential of smallholder farms in Kenya

Smallholder farmers represent the majority of food producers around the world, yet they are often the most at risk of suffering yield gaps and not achieving their production potential. Ecological Intensification (EI) is a knowledge intensive approach to sustainable agricultural intensification which utilises biodiversity-based ecosystem services to support greater yield and reduce reliance on agrochemical inputs. Despite the potential benefit of EI based practices, uptake by smallholders is not as widespread as it could be. Here we test the hypothesis that application of EI on smallholder farms in Kenya is a viable approach that could be taken in order to enhance food security. Focusing on natural pest control and crop pollination, we used farmer surveys to explore the potential for EI in central Kenya. We identified to what extent farm typology and access to knowledge determine the incentives and barriers facing smallholder producers and how this influences optimal pathways for sharing knowledge and providing extension services. We found considerable potential for EI of smallholder farms in this region; most farmers grew insect pollinated crops and some farmers already employed EI practices, while others relied heavily on chemical pesticides. Based on physical, social and economic factors, three farm typologies emerged including ‘semi-commercial’, ‘market orientated’ and ‘subsistence’. These typologies influenced the appropriate EI practices available to farmers, as well as routes through which knowledge was shared and the extent to which extension services were utilised. We propose that to support effective uptake of EI practices, smallholder farm heterogeneity should be acknowledged and characterised in order to target the needs and capabilities of farmers and identify appropriate knowledge sharing and support pathways. The approach we take here has the potential to be employed in other regions globally

Cryptococcal Antigenemia in Human Immunodeficiency Virus Antiretroviral Therapy-Experienced Ugandans With Virologic Failure.

BACKGROUND: Detectable serum or plasma cryptococcal antigen (CrAg) precedes symptomatic cryptococcal meningitis. The World Health Organization recommends CrAg screening for human immunodeficiency virus-positive persons with CD4 count <100 cells/μL initiating antiretroviral therapy (ART). However, an increasing proportion of patients with cryptococcosis are now ART experienced. Whether CrAg screening is cost-effective in those with virologic failure is unknown. METHODS: We retrospectively performed nationwide plasma CrAg testing among ART-experienced Ugandan adults with virologic failure (≥1000 copies/mL) using leftover plasma after viral load testing during September 2017-January 2018. For those who were CrAg positive, we obtained ART history, meningitis occurrence, and 6-month survival via medical records review. RESULTS: Among 1186 subjects with virologic failure, 35 (3.0%) were CrAg positive with median ART duration of 41 months (interquartile range, 10-84 months). Among 25 subjects with 6-month outcomes, 16 (64%) survived, 7 (28%) died, and 2 (8%) were lost. One survivor had suffered cryptococcal meningitis 2 years prior. Two others developed cryptococcal meningitis and survived. Five survivors were known to have received fluconazole. Thus, meningitis-free survival at 6 months was 61% (14/23). Overall, 91% (32/35) of CrAg-positive persons had viral load ≥5000 copies/mL compared with 64% (735/1151) of CrAg-negative persons (odds ratio, 6.0 [95% confidence interval, 1.8-19.8]; P = .001). CrAg prevalence was 4.2% (32/768) among those with viral loads ≥5000 copies/mL and 0.7% (3/419) among those with viral loads <5000 copies/mL. CONCLUSIONS: In addition to the CD4 threshold of <100 cells/μL, reflexive CrAg screening should be considered in persons failing ART in Uganda with viral loads ≥5000 copies/mL

Prioritization of invasive alien species with the potential to threaten agriculture and biodiversity in Kenya through horizon scanning

Invasive alien species (IAS) rank among the most significant drivers of species extinction and ecosystem degradation resulting in significant impacts on socio-economic development. The recent exponential spread of IAS in most of Africa is attributed to poor border biosecurity due to porous borders that have failed to prevent initial introductions. In addition, countries lack adequate information about potential invasions and have limited capacity to reduce the risk of invasions. Horizon scanning is an approach that prioritises the risks of potential IAS through rapid assessments. A group of 28 subject matter experts used an adapted methodology to assess 1700 potential IAS on a 5-point scale for the likelihood of entry and establishment, potential socio-economic impact, and impact on biodiversity. The individual scores were combined to rank the species according to their overall potential risk for the country. Confidence in individual and overall scores was recorded on a 3-point scale. This resulted in a priority list of 120 potential IAS (70 arthropods, 9 nematodes, 15 bacteria, 19 fungi/chromist, 1 viroid, and 6 viruses). Options for risk mitigation such as full pest risk analysis and detection surveys were suggested for prioritised species while species for which no immediate action was suggested, were added to the plant health risk register and a recommendation was made to regularly monitor the change in risk. By prioritising risks, horizon scanning guides resource allocation to interventions that are most likely to reduce risk and is very useful to National Plant Protection Organisations and other relevant stakeholders

Spatial and temporal transcriptomic analysis of the Arabidopsis thaliana–Botrytis cinerea interaction

Plants activate an array of defence responses following recognition of pathogenic organisms. This study attempted to characterize at a transcriptional level, the defence responses of Arabidopsis thaliana after infection with Botrytis cinerea using microarrays. Alteration in transcript levels following infection was investigated in time (temporal) and space (spatial). A number of genes were up- and down-regulated specifically at 12 h, others at 24 h while others were up- and down-regulated at both time points. Similarly, some genes were specifically induced very close to the lesion while others in more distal tissue. Clustering of expression profiles resulting from other biotic and abiotic interactions with Arabidopsis indicated a large overlap in gene expression. This study highlighted a multitude of genes induced in Arabidopsis spatially and temporally following infection with B. cinerea providing an insight into key processes of defence against this pathogen. The plethora of altered genes identified are candidates for further investigation

Proteomic analysis of the Arabidopsis thaliana-Botrytis cinerea interaction using two-dimensional liquid chromatography

A two-dimensional liquid chromatography (2D LC) system, ProteomeLab PF 2D, was employed to study the defence proteome of Arabidopsis following infection with the necrotrophic fungal pathogen, Botrytis cinerea. This system demonstrated differential protein expression in control and treated samples in some fractions. However, the amount of proteins in the fractions and the level to which they were changing could not be established. Among the proteins identified in the fractions that displayed an increase in absorbance was catalase 3 and glutathione S-transferases, demonstrating the importance of an antioxidant system in defence against B. cinerea. Most of the proteins were identified in fractions that displayed reduction in absorbance. Functional categorisation of the identified proteins demonstrated the overrepresentation of photosynthetic pathway, a phenomenon also observed in other host and nonhost pathogen interactions. Proteomelab PF 2D did not identify as many proteins as expected possibly due to the masking effect of ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO) as this protein was identified in almost all fractions including those having an increase in absorbance. Depletion of this protein from crude plant protein extracts is likely to improve protein identification by mass spectrometry, especially for the low abundant proteins. A number of proteins were identified in each fraction and it was difficult to discern which of the proteins was responsible for the differential increase or reduction in absorbance

Characterization of isolates that cause black rot of crucifers in East Africa

A study was conducted in the East African countries of Kenya, Tanzania and Uganda in the months of July and August 2009 with the objectives of assessing the status of black rot and race structure of Xanthomonas campestris pv. campestris in the three countries. Samples infected with black rot were collected from farmers’ fields mainly from Brassica oleracea crops (broccoli, cabbage, cauliflower and kales). A total of 399 farms were surveyed of which 260 were from Kenya, 91 from Tanzania and 48 from Uganda. Following successful isolations, a total of 249 isolates of the causal agent, Xanthomonas campestris pv. campestris were recovered. Pathogenicity of all isolates was confirmed on B. oleracea susceptible cultivars Copenhagen Market F1 and Wirosa F1. Sixty of the 250 isolates were race-typed using a differential set Brassica spp. Only two races, 1 (Kenya and Tanzania) and 4 (Kenya, Tanzania and Uganda) were observed however, another race (5) was observed from one isolate recovered from a B. rapa sample obtained from Tanzania in 2003. Genomic fingerprinting with repetitive-PCR revealed clusters that did not depict significant correlations between isolates and geographical location, isolates and host adaptation or isolates and race. However, it did demonstrate existence of genetic differences within the East African X. campestris pv. campestris population indicating that it is not a similar clonal population of the same genetic background

African women and young people as agriculture service providers—business models, benefits, gaps and opportunities

Abstract We use a combination of a global desk review of the literature with information from an on-going action research in Kenya to provide insights into the main characteristics, benefits and shortfalls of business models for engaging women and young people in agricultural service provision in Africa. The findings demonstrate that the engagement of African women and young people in agricultural service provision is not a panacea to the challenges they face. However various business models have been successful in contributing to economic empowerment, to increasing entrepreneurial activities and to upskilling of women and young people engaged as service providers. Business models that are successful are place-based and people-focused, market-driven and focused on value chains. Challenges however abound due to various factors, hence for sustainability there is need for multi-sectoral inter-institutional collaboration that pulls in funding and which makes a case for private sector buy-in. Future research should focus on increasing the evidence base to understand if successes with inclusion of women and young people in agricultural service provision has an influence on emerging agricultural policy. Research should also rigorously assess the extent to which successful agricultural service provision business models are engendered, provide sufficient levels of renumeration and the extent to which they impact farmer outcomes