scholarly journals Tree Lab: Portable genomics for early detection of plant viruses and pests in Sub-Saharan Africa

2019 ◽  
Author(s):  
Laura M. Boykin ◽  
Peter Sseruwagi ◽  
Titus Alicai ◽  
Elijah Ateka ◽  
Ibrahim Umar Mohammed ◽  
...  
Keyword(s):  
Real Time ◽  
Animal Health ◽  
Plant Viruses ◽  
Sub Saharan Africa ◽  
Dna Purification ◽  
Processing Unit ◽  
Sample Collection ◽  
African Countries ◽  
On Farm

AbstractIn this case study we successfully teamed the PDQeX DNA purification technology developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices developed by Oxford Nanopore Technologies to produce an effective point-of-need field diagnostic system. The PDQeX extracts DNA using a cocktail of thermophilic proteinases and cell wall degrading enzymes, thermo-responsive extractor cartridges and a temperature control unit. This single-step closed system delivers purified DNA with no cross contamination. The MinIT is a newly released data processing unit that converts MinION raw signal output into base called data locally in real time, removing the need for high specification computers and large file transfers from the field. All three devices are battery powered with an exceptionally small footprint that facilitates transport and set up.To evaluate and validate capability of the system for unbiased pathogen identification by realtime sequencing in a farmer’s field setting, we analysed samples collected from cassava plants grown by subsistence farmers in three sub-Sahara African countries (Tanzania, Uganda and Kenya). A range of viral pathogens, all with similar symptoms, greatly reduce yield or completely destroy cassava crops. 800 million people worldwide depend on cassava for food and yearly income, and viral diseases are a significant constraint on its production (https://cassavavirusactionproject.com). Early pathogen detection at a molecular level has great potential to rescue crops within a single growing season by providing results that inform decisions on disease management, use of appropriate virus resistant or replacement planting.This case study presented conditions of working in-field with limited or no access to mains power, laboratory infrastructure, internet connectivity and highly variable ambient temperature. An additional challenge is that, generally, plant material contains inhibitors of downstream molecular processes making effective DNA purification critical. We successfully undertook real-time on-farm genome sequencing of samples collected from cassava plants on three farms, one in each country. Cassava mosaic begomoviruses were detected by sequencing leaf, stem, tuber and insect samples. The entire process, from arrival on farm to diagnosis including sample collection, processing and provisional sequencing results was complete in under 4 hours. The need for accurate, rapid and on-site diagnosis grows as globalized human activity accelerates. This technical breakthrough has applications that are relevant to human and animal health, environmental management and conservation.

scholarly journals Tree Lab: Portable genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 632 ◽  
Author(s):  
Boykin ◽  
Sseruwagi ◽  
Alicai ◽  
Ateka ◽  
Mohammed ◽  
...  
Keyword(s):  
Real Time ◽  
Animal Health ◽  
Plant Viruses ◽  
Sub Saharan Africa ◽  
Dna Purification ◽  
Processing Unit ◽  
Sample Collection ◽  
African Countries ◽  
On Farm

In this case study we successfully teamed the PDQeX DNA purification technology developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices developed by Oxford Nanopore Technologies to produce an effective point-of-need field diagnostic system. The PDQeX extracts DNA using a cocktail of thermophilic proteinases and cell wall-degrading enzymes, thermo-responsive extractor cartridges and a temperature control unit. This closed system delivers purified DNA with no cross-contamination. The MinIT is a newly released data processing unit that converts MinION raw signal output into nucleotide base called data locally in real-time, removing the need for high-specification computers and large file transfers from the field. All three devices are battery powered with an exceptionally small footprint that facilitates transport and setup. To evaluate and validate capability of the system for unbiased pathogen identification by real-time sequencing in a farmer’s field setting, we analysed samples collected from cassava plants grown by subsistence farmers in three sub-Sahara African countries (Tanzania, Uganda and Kenya). A range of viral pathogens, all with similar symptoms, greatly reduce yield or destroy cassava crops. Eight hundred (800) million people worldwide depend on cassava for food and yearly income, and viral diseases are a significant constraint to its production. Early pathogen detection at a molecular level has great potential to rescue crops within a single growing season by providing results that inform decisions on disease management, use of appropriate virus-resistant or replacement planting. This case study presented conditions of working in-field with limited or no access to mains power, laboratory infrastructure, Internet connectivity and highly variable ambient temperature. An additional challenge is that, generally, plant material contains inhibitors of downstream molecular processes making effective DNA purification critical. We successfully undertook real-time on-farm genome sequencing of samples collected from cassava plants on three farms, one in each country. Cassava mosaic begomoviruses were detected by sequencing leaf, stem, tuber and insect samples. The entire process, from arrival on farm to diagnosis, including sample collection, processing and provisional sequencing results was complete in under 3 h. The need for accurate, rapid and on-site diagnosis grows as globalized human activity accelerates. This technical breakthrough has applications that are relevant to human and animal health, environmental management and conservation.

A critical analysis of water PPP failures in sub-Saharan Africa

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Salman Tariq ◽  
Xueqing Zhang
Keyword(s):  
Construction Management ◽  
Design Methodology ◽  
Sub Saharan Africa ◽  
African Countries ◽  
Content Type ◽  
Rigorous Approach ◽  
First Case ◽  
Management Perspective ◽  
Sub Saharan

PurposeTop-down pressure from donors, public sector inefficiencies and fund deficits have steered the introduction of public–private partnerships (PPPs) in sub-Saharan Africa. However, PPP activities in the water sector have been quite insignificant compared to other infrastructure sectors in this region. In addition, a number of water PPPs have encountered great difficulties and subsequent failures. This study aims at unveiling the underlying reasons behind failures.Design/methodology/approachThis study has classified the failure types of water PPPs and reviewed the development of water PPPs in sub-Saharan Africa to identify failed ones. Eight failed case studies are completed through the rigorous approach of event sequence mapping.FindingsNine root causes of water PPP failure are identified through a thorough examination of these failed water PPP cases and the interrelationships between these failure causes are established. The failure causes are further generalized through literature focusing on water PPP failures in developing countries and problematic issues that hinder the implementation of successful water PPPs across different Sub-Saharan African countries. Recommendations are provided for future improvements in carrying out water PPPs in Sub-Saharan Africa by learning past lessons and drawing experiences.Originality/valueThis is the first case study on water PPP failures in Sub-Saharan Africa from a construction management perspective. This study will help governments and the private sector in developing stronger future water PPPs.

ICT in Education Development in Africa

2011 ◽  
pp. 283-305
Author(s):  
Chijioke J. Evoh
Keyword(s):  
Education Policy ◽  
Interest Groups ◽  
Policy Process ◽  
Teaching And Learning ◽  
Sub Saharan Africa ◽  
Ict In Education ◽  
African Countries ◽  
Education Development ◽  
Sub Saharan

This study presents the rationale for policy and institutional frameworks in the development of ICT in secondary education in countries in Sub-Saharan Africa (SSA). As the adoption of modern ICTs slowly gain momentum, various stakeholders in education have recognized the importance of leveraging these technological tools for the improvement of teaching and learning. To a large extent, the application of modern ICTs in education remains uncoordinated in many countries. This study identifies the institutional framework as the dominant approach to ICT in education policy process in the region. This involves the participation of broad-based interest groups in the policy process. Using South Africa as a case study, the study presents elements of ICT in education policy as well as policy lessons that would enable African countries use ICTs for productive educational outcomes.

Evaluation of two point of care technologies for measuring monoclonal antibody therapeutic-A concentrations in blood

Bioanalysis ◽  
2020 ◽  
Vol 12 (20) ◽  
pp. 1449-1458
Author(s):  
Saloumeh K Fischer ◽  
Kathi Williams ◽  
Ian Harmon ◽  
Bryan Bothwell ◽  
Hua Xu ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Real Time ◽  
Point Of Care ◽  
Turnaround Time ◽  
Monitoring Methods ◽  
Sample Collection ◽  
Time Data ◽  
Serum Samples ◽  
Quick Turnaround Time

Aim: Current blood monitoring methods require sample collection and testing at a central lab, which can take days. Point of care (POC) devices with quick turnaround time can provide an alternative with faster results, allowing for real-time data leading to better treatment decisions for patients. Results/Methodology: An assay to measure monoclonal antibody therapeutic-A was developed on two POC devices. Data generated using 75 serum samples (65 clinical & ten spiked samples) show correlative results to the data generated using Gyrolab technology. Conclusion: This case study uses a monoclonal antibody therapeutic-A concentration assay as an example to demonstrate the potential of POC technologies as a viable alternative to central lab testing with quick results allowing for real-time decision-making.

Condom social marketing in sub-Saharan Africa and the Total Market Approach

Sexual Health ◽  
2012 ◽  
Vol 9 (1) ◽  
pp. 44 ◽  
Author(s):  
Steven Chapman ◽  
Krishna Jafa ◽  
Kim Longfield ◽  
Nadja Vielot ◽  
Justin Buszin ◽  
...  
Keyword(s):  
Condom Use ◽  
Market Share ◽  
Social Marketing ◽  
Sub Saharan Africa ◽  
African Countries ◽  
Market Approach ◽  
Condom Social Marketing ◽  
Over Time ◽  
Total Market

Background Social marketing interventions are important in developing nations. Both increasing use and shifting users from receiving subsidised condoms need to be pursued using a Total Market Approach (TMA). This paper reviews the performance of social marketing through a cross-country comparison of condom use, equity and market share, plus a case study illustrating how TMA can be applied. Methods: Demographic and Health Survey data (1998–2007) provide condom use trends, concentration indices and sources of supply by gender for 11 African countries. Service delivery information and market research provide market share data for the same period. For the case study, two-yearly surveys (2001–09) are the source of condom trends, and retail audit data (2007–09) provide sustainability data. Results: Among women, condom use with a non-marital, non-cohabiting partner increased significantly in 7 of 11 countries. For men, 5 of 11 countries showed an increase in condom use. Equity improved for men in five countries and was achieved in two; for women, equity improved in three. Most obtained condoms from shops and pharmacies; social marketing was the dominant source of supply. Data from Kenya were informative for TMA, showing improvements in condom use over time, but sustainability results were mixed and equity was not measured. Overall market value and number of brands increased; however, subsidies increased over time. Conclusions: Condom social marketing interventions have advanced and achieved the goals of improving use and making condoms available in the private sector. It is time to manage interventions and influence markets to improve equity and sustainability.

scholarly journals Using data-driven approaches to improve delivery of animal health care interventions for public health

2021 ◽  
Vol 118 (5) ◽  
pp. e2003722118
Author(s):  
Stella Mazeri ◽  
Jordana L. Burdon Bailey ◽  
Dagmar Mayer ◽  
Patrick Chikungwa ◽  
Julius Chulu ◽  
...  
Keyword(s):  
Real Time ◽  
Vaccination Coverage ◽  
Large Scale ◽  
Animal Health ◽  
Vaccination Campaign ◽  
Sub Saharan Africa ◽  
Data Driven ◽  
Time Data ◽  
Real Time Analysis ◽  
Vaccination Campaigns

Rabies kills ∼60,000 people per year. Annual vaccination of at least 70% of dogs has been shown to eliminate rabies in both human and canine populations. However, delivery of large-scale mass dog vaccination campaigns remains a challenge in many rabies-endemic countries. In sub-Saharan Africa, where the vast majority of dogs are owned, mass vaccination campaigns have typically depended on a combination of static point (SP) and door-to-door (D2D) approaches since SP-only campaigns often fail to achieve 70% vaccination coverage. However, D2D approaches are expensive, labor-intensive, and logistically challenging, raising the need to develop approaches that increase attendance at SPs. Here, we report a real-time, data-driven approach to improve efficiency of an urban dog vaccination campaign. Historically, we vaccinated ∼35,000 dogs in Blantyre city, Malawi, every year over a 20-d period each year using combined fixed SP (FSP) and D2D approaches. To enhance cost effectiveness, we used our historical vaccination dataset to define the barriers to FSP attendance. Guided by these insights, we redesigned our vaccination campaign by increasing the number of FSPs and eliminating the expensive and labor-intensive D2D component. Combined with roaming SPs, whose locations were defined through the real-time analysis of vaccination coverage data, this approach resulted in the vaccination of near-identical numbers of dogs in only 11 d. This approach has the potential to act as a template for successful and sustainable future urban SP-only dog vaccination campaigns.

scholarly journals Real time portable genome sequencing for global food security

2018 ◽  
Author(s):  
Laura M. Boykin ◽  
Ammar Ghalab ◽  
Bruno Rossitto De Marchi ◽  
Anders Savill ◽  
James M. Wainaina ◽  
...  
Keyword(s):  
Real Time ◽  
Crop Production ◽  
High Throughput Sequencing ◽  
Smallholder Farmers ◽  
Plant Viruses ◽  
Sub Saharan Africa ◽  
Global Food Security ◽  
Detection And Identification ◽  
Sub Saharan ◽  
Zero Hunger

AbstractThe United Nations has listed Zero Hunger as one of the 17 global sustainable development goals to end extreme poverty by 2030. Plant viruses are a major constraint to crop production globally causing an estimated $30 billion in damage 1 leaving millions of people food insecure 2. In Africa, agriculture employs up to 50% of the workforce, yet only contributes 15% to the GDP on average 3, suggesting that there is low productivity and limited value addition. This can be addressed through continued innovation in the fields of science and technology as suggested in the Science Agenda for Agriculture in Africa (S3A) 4. Sustainable management of plant viruses and their associated vectors must include efficient diagnostics for surveillance, detection and identification to inform disease management, including the development and strategic deployment of virus resistant varieties. To date, researchers have been utilizing conventional methods such as; PCR, qPCR, high throughput sequencing (RNA-Seq, DNA-Seq) and Sanger sequencing for pathogen identification. However, these methods are both costly and time consuming, delaying timely control actions. The emergence of new tools for real-time diagnostics, such as the Oxford Nanopore MinION, have recently proven useful for early detection of Ebola 6 and Zika 7,8, even in low resourced laboratories. For the first time globally, the MinION portable pocket DNA sequencer was used to sequence whole plant virus genomes. We used this technology to identify the begomoviruses causing the devastating CMD which is ravaging smallholder farmers’ crops in sub-Saharan Africa. Cassava, a carbohydrate crop from which tapioca originates, is a major source of calories for over eight hundred (800) million people worldwide. With this technology, farmers struggling with diseased crops can take immediate, restorative action to improve their livelihoods based on information about the health of their plants, generated using a portable, real-time DNA sequencing device.

Grievances, governance and Islamist violence in sub-Saharan Africa

2015 ◽  
Vol 53 (4) ◽  
pp. 505-531 ◽  
Author(s):  
Caitriona Dowd
Keyword(s):  
Political Violence ◽  
Sub Saharan Africa ◽  
Security Threat ◽  
African Countries ◽  
Political Exclusion ◽  
History Of ◽  
Triggering Events ◽  
Sub Saharan ◽  
Conflict Research

AbstractWhat explains the emergence of Islamist violence as a substantial security threat in such diverse contexts as Kenya, Mali and Nigeria? This article addresses this question through an exploration of the strategies of governance employed by states, and how these shape the emergence and mode of collective violence. Conflict research often emphasises the specificity of Islamist violence; but these conflicts can be understood as a form of political exclusion and grievance-based violence, comparable to other forms of political violence. Further, violent Islamist groups emerge from local conditions: the areas in which groups are established share similar local experiences of governance and political marginalisation; a history of violent conflict on which Islamist militants capitalise; and key triggering events expanding or reinforcing state exclusion. These findings challenge a narrative emphasising the global, interconnected nature of Islamist violence. This article pairs data from the Armed Conflict Location & Event Dataset (ACLED) with Afrobarometer survey data and case study evidence to identify drivers of Islamist violence across three African countries.

Prevalence of Yersinia enterocolitica in Market Weight Hogs in the United States†

2008 ◽  
Vol 71 (6) ◽  
pp. 1162-1168 ◽  
Author(s):  
IRENE V. WESLEY ◽  
SAUMYA BHADURI ◽  
ERIC BUSH
Keyword(s):  
Real Time ◽  
Yersinia Enterocolitica ◽  
Real Time Pcr ◽  
Management Practices ◽  
Animal Health ◽  
The United States ◽  
Individual Animal ◽  
Enrichment Broth ◽  
Fecal Samples ◽  
On Farm

Pigs are the major animal reservoir for Yersinia enterocolitica strains, which are potentially pathogenic for humans. The goals of this study were (i) to estimate the individual animal and on-farm prevalences of Y. enterocolitica in hogs based on tonsil samples collected during National Animal Health Monitoring System Swine 2002 study and (ii) to use these data with data previously published for fecal samples to determine on-farm risk factors for Y. enterocolitica. Tonsil swabs (1,218) and fecal samples (2,847) were collected on 124 farms located in the top 17 pork-producing states. Ten percent of tonsils (122 of 1,218 samples) were positive in irgasan-tiracillin-chlorate (ITC) enrichment broth by real-time PCR, but only 5.6% of samples (68 of 1,218) were positive after subculture on the more selective cefsulodin-irgasan-novobiocin (CIN) agar. For tonsils, the on-farm prevalence based on real-time PCR detection of the ail gene in ITC enrichment broth cultures was 32% (32 of 100 premises sampled); the prevalence based on subculture in CIN agar was 19.6% (20 of 102 premises). Results of bacteriological isolation and real-time PCR analysis of tonsils and feces were combined to estimate prevalence (individual animal and farm), which was subsequently correlated with 40 farm management practices. Four factors and their accompanying odds ratios (ORs) were identified in the final regression model: location in a central state (OR =0.3), vaccination for Escherichia coli (OR = 3.0), percentage of deaths due to scours (OR = 3.5), and presence of meat or bone meal in grower-finisher diet (OR = 4.1).

Highlights on a UNESCO/Sida project to assess the environmental and health challenges of mining activities in Sub-Saharan Africa

2020 ◽  
Author(s):  
Toteu S. Félix
Keyword(s):  
International Development ◽  
Environmental Governance ◽  
Animal Health ◽  
Development Cooperation ◽  
Sub Saharan Africa ◽  
Mining Activities ◽  
African Countries ◽  
Continental Scale ◽  
Sub Saharan ◽  
The Impact

<p>Mining is an important pillar of economic growth of many African countries. However, problems arising from this activity pose serious challenges, which most of these countries have difficulties to address properly because of poor environmental governance as highlighted in the Africa Mining Vision. Many African countries also lack a precise inventory and assessment of environmental impacts of abandoned and derelict mines. As a consequence, there is an urgent need to evaluate the true extent of the detrimental effects of metal and metalloid pollutants and their impact on human and animal health, as well as on ecosystems. Between 2013 and 2017 and thanks to a Partnership Programme between UNESCO and the Swedish International Development Cooperation Agency (Sida), a network of over 100 Earth scientists from 29 Africa assessed the impacts of mining activities in sub-Saharan Africa. The project intended to provide crucial scientific knowledge that will contribute to understanding the factors that control cycling of pollutants from mine sites (abandoned or active) to soils, water and vegetation and the impact on the food chain. We anticipate that the results of the project will be used to improve the environmental norms in individual countries in Sub-Saharan Africa and the efficiency of governments in addressing the challenges related to the adverse effects of mining activities. The preliminary results of the project have recently been published as a Special Issue in the Journal of Geochemical Exploration. During the presentation, we intend to highlight few examples where mining activities alone or in interaction geological background are contributing to threat the ecosystem and health of neighbouring communities. We will also draw the lessons learnt from the implementation of this continental-scale project.</p>

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