Farming for impact - a case study of smallholder agriculture in Rwanda

This case study demonstrates that with targeted support and favourable policy conditions, resource-poor farmers can increase their productivity and contribute to hunger and poverty reduction goals. Findings indicate that the Government of Rwanda (GoR) has invested in smallholder farming and as a result, agricultural productivity and output has increased in the country. These increases have partially insulated Rwanda from food price spikes in East Africa and led to general food availability increasing in the country

On trial: agricultural biotechnology in Africa

Increasing agricultural productivity and adapting farming to climate change are central to Africa’s development prospects. There are important opportunities to enhance yields and increase resilience through the adoption of improved crop varieties. In some cases, biotechnology, and in particular genetic modification (GM), offers advantages over conventional plant-breeding approaches. Accordingly there are a various projects under way to develop new GM varieties for African farmers, ranging from drought-resistant maize to varieties of cassava, banana, sorghum, cowpea and sweet potato with resistance to pests and disease. In addition to government funds, these projects have also attracted the support of influential donor agencies and philanthropic foundations. However, despite the expenditure of considerable resources, the potential of GM in Africa is not being realized. So far no GM trait developed for African farmers has been put to use. Multiple barriers inhibit the development and adoption of pro-poor GM varieties in Africa. On the demand side, farmers may be reluctant to adopt GM varieties owing to a lack of export opportunities and distrust of the technology among local consumers. Farmers may also be concerned about exploitation by transnational seed companies (despite the fact that development of new GM technologies in Africa is dominated by the public sector). On the supply side, donor funding struggles to match the long timescales of research and development, while incentives among research scientists may be poorly aligned with farmer outcomes. Non-existent, poorly functioning or overly punitive regulatory regimes discourage investment. The most important barriers – such as regulatory constraints, consumer distrust and weak farmer demand – must be understood in the context of wider social and political dynamics surrounding GM, typified by misinformation, polarized public discourse, and dysfunctional and opportunistic politics. The result is most GM projects becoming ‘stuck’ at the field trial stage without ever progressing to release. This ‘convenient deadlock’ of continual field trials allows governments to manage political risks by effectively balancing the demands of pro-GM and anti-GM lobbies – proponents of GM have a pipeline of technologies, while opponents are appeased by the failure of any to gain approval. The disabling socio-political environment for GM development in Africa greatly reduces the efficacy of investment in this technology. This has two important implications. First, technology development needs to be located within a wider project of transformation that engages key actors – most notably politicians, policy-makers and farmers – as stakeholders from the outset, and includes strategies to address multiple demand- and supply-side barriers. Second, successful adoption is more likely in countries with less disabling political conditions, characterized by lower levels of consumer distrust and opposition, genuine farmer demand and demonstrable commitment from government. Focusing efforts and resources on a small number of ‘best bet’ countries will also allow donors and technology providers to support more ambitious, transformational projects led by national governments

Molecular Techniques Reveal Wide Phyletic Diversity of Heterotrophic Microbes Associated with Discodermia spp. (Porifera: Demospongiae)

Sponges are well known to harbor large numbers of heterotrophic microbes within their mesohyl. Studies to determine the diversity of these associated microbes have been attempted for only a few shallow water species. We cultured various microorganisms from several species of Discodermia collected from deep water using the \u27Johnson-Sea-Link\u27 manned submersibles, and characterised them by standard microbiological identification methods. Characterisation of a small proportion (ca. 10%) of the total and potential eubacterial isolate collection with molecular systematics techniques revealed a wide diversity of microbes. Phylogenetic analyses of 32 small subunit (SSU) 16S-like rRNA gene sequences from different micorbes indicated high levels of taxonomic diversity assoiated with this genus of sponge. For example, bacteria from at least five cubacterial subdivisions - gamma, alpha, beta, Cytophaga and Gram positive - were isolated from the mesohyl of Discodermia. Several strains were unidentifiable from current sequence databases. No overlap was found between sequences of 24 isolates and 8 sequences obtained by PCR and cloning directly from sponge samples. The abundance and diversity of microbes associated with sponges such as Discodermia suggest that they may play important roles in marine microbial ecology, dispersal and evolution

Soil health metrics reflect yields in long-term cropping system experiments

Soil health metrics with strong links to ecological function and agricultural productivity are needed to ensure that future management of agricultural systems meets sustainability goals. While ecological metrics and crop yields are often considered separately from one another, our work sought to assess the links between the two in an agricultural context where productivity is a key consideration. Here, we investigated the value of soil health tests in terms of their relevance to agricultural management practices and crop yields at contrasting long term cropping systems experiments. One site was on a sandy loam Leptic Podzol and the other on a sandy clay loam Endostagnic Luvisol. Furthermore, the experiments had different management systems. One contained legume-supported rotations with different grass-clover ley durations and organic amendment usage, while the other compared a range of nutrient input options through fertiliser and organic amendments on the same rotation without ley periods. Metrics included field tests (earthworm counts and visual evaluation of soil structure scores) with laboratory analysis of soil structure, chemistry and biology. This analysis included bulk density, macroporosity, pH, available phosphorus, exchangeable potassium, soil organic matter and potentially mineralizable nitrogen. Using a novel combination of long-term experiments, management systems and distinctive soil types, we demonstrated that as well as providing nutrients, agricultural management which resulted in better soil organic matter, pH, potassium and bulk density was correlated with higher crop yields. The importance of ley duration and potentially mineralizable nitrogen to yield in legume-supported systems showed the impact of agricultural management on soil biology. In systems with applications of synthetic fertiliser, earthworm counts and visual evaluation of soil structure scores were correlated with higher yields. We concluded that agricultural management altered yields not just through direct supply of nutrients to crops, but also through the changes in soil health measured by simple metrics

New approach combining food value with nutrient budgeting provides insights into the value of alternative farming systems

Sustainable farming systems provide food for humans while balancing nutrient management. Inclusion or exclusion of livestock has nutrient management implications, as livestock produce food from otherwise inedible crops and their manure is a valuable soil conditioner. However, plant-based diets are becoming more widespread due to perceived environmental benefits. We measure both food production in terms of nourishment to humans (in this study measured by protein, fat, starch and sugar production) and nutrient sustainability in terms of fertiliser use of six rotational farming systems with differences in nutrient management approaches. The arable practices included were the application of synthetic fertilisers, a range of organic amendments, incorporation of crop residues and legume cultivation. Livestock and associated products were included in some systems but excluded in others. The production of protein, fat, starch and sugar was combined with the balance of nitrogen (N), phosphorus (P) and potassium (K) into an overall measure of nutrient use efficiency of human macronutrient production. Across all systems considered, N use efficiency (5-13 kg protein/kg applied N) was lower than P (84-772 kg protein/kg applied P) or K (63-2060 kg protein/kg applied K), and combining synthetic fertiliser use with organic amendment applications raised production significantly while balancing P and K management, regardless of which organic amendment was used. Legume-supported rotations without livestock produced more protein, starch and sugar per unit area than those with livestock. Nutrient balances and nutrient use efficiencies were more sensitive to management changes than purely food production. Using this approach allowed us to identify areas for improvement in food production based on the specific nutritional value of offtakes as opposed to yield overall

New approach combining food value with nutrient budgeting provides insights into the value of alternative farming systems

Sustainable farming systems provide food for humans while balancing nutrient management. Inclusion or exclusion of livestock has nutrient management implications, as livestock produce food from otherwise inedible crops and their manure is a valuable soil conditioner. However, plant-based diets are becoming more widespread due to perceived environmental benefits. We measure both food production in terms of nourishment to humans (in this study measured by protein, fat, starch and sugar production) and nutrient sustainability in terms of fertiliser use of six rotational farming systems with differences in nutrient management approaches. The arable practices included were the application of synthetic fertilisers, a range of organic amendments, incorporation of crop residues and legume cultivation. Livestock and associated products were included in some systems but excluded in others. The production of protein, fat, starch and sugar was combined with the balance of nitrogen (N), phosphorus (P) and potassium (K) into an overall measure of nutrient use efficiency of human macronutrient production. Across all systems considered, N use efficiency (5-13 kg protein/kg applied N) was lower than P (84-772 kg protein/kg applied P) or K (63-2060 kg protein/kg applied K), and combining synthetic fertiliser use with organic amendment applications raised production significantly while balancing P and K management, regardless of which organic amendment was used. Legume-supported rotations without livestock produced more protein, starch and sugar per unit area than those with livestock. Nutrient balances and nutrient use efficiencies were more sensitive to management changes than purely food production. Using this approach allowed us to identify areas for improvement in food production based on the specific nutritional value of offtakes as opposed to yield overall.Peer reviewe

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis

Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century

The diagnosis of rabies is routinely based on clinical and epidemiological information, especially when exposures are reported in rabies-endemic countries. Diagnostic tests using conventional assays that appear to be negative, even when undertaken late in the disease and despite the clinical diagnosis, have a tendency, at times, to be unreliable. These tests are rarely optimal and entirely dependent on the nature and quality of the sample supplied. In the course of the past three decades, the application of molecular biology has aided in the development of tests that result in a more rapid detection of rabies virus. These tests enable viral strain identification from clinical specimens. Currently, there are a number of molecular tests that can be used to complement conventional tests in rabies diagnosis. Indeed the challenges in the 21st century for the development of rabies diagnostics are not of a technical nature; these tests are available now. The challenges in the 21st century for diagnostic test developers are two-fold: firstly, to achieve internationally accepted validation of a test that will then lead to its acceptance by organisations globally. Secondly, the areas of the world where such tests are needed are mainly in developing regions where financial and logistical barriers prevent their implementation. Although developing countries with a poor healthcare infrastructure recognise that molecular-based diagnostic assays will be unaffordable for routine use, the cost/benefit ratio should still be measured. Adoption of rapid and affordable rabies diagnostic tests for use in developing countries highlights the importance of sharing and transferring technology through laboratory twinning between the developed and the developing countries. Importantly for developing countries, the benefit of molecular methods as tools is the capability for a differential diagnosis of human diseases that present with similar clinical symptoms. Antemortem testing for human rabies is now possible using molecular techniques. These barriers are not insurmountable and it is our expectation that if such tests are accepted and implemented where they are most needed, they will provide substantial improvements for rabies diagnosis and surveillance. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis

Impacts of Poultry House Environment on Poultry Litter Bacterial Community Composition

Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly Gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens

Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects

Estimates from genome-wide association studies (GWAS) of unrelated individuals capture effects of inherited variation (direct effects), demography (population stratification, assortative mating) and relatives (indirect genetic effects). Family-based GWAS designs can control for demographic and indirect genetic effects, but large-scale family datasets have been lacking. We combined data from 178,086 siblings from 19 cohorts to generate population (between-family) and within-sibship (within-family) GWAS estimates for 25 phenotypes. Within-sibship GWAS estimates were smaller than population estimates for height, educational attainment, age at first birth, number of children, cognitive ability, depressive symptoms and smoking. Some differences were observed in downstream SNP heritability, genetic correlations and Mendelian randomization analyses. For example, the within-sibship genetic correlation between educational attainment and body mass index attenuated towards zero. In contrast, analyses of most molecular phenotypes (for example, low-density lipoprotein-cholesterol) were generally consistent. We also found within-sibship evidence of polygenic adaptation on taller height. Here, we illustrate the importance of family-based GWAS data for phenotypes influenced by demographic and indirect genetic effects