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BecA-ILRI Hub: Mobilizing biosciences for Africa’s development


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Presented by Jagger Harvey, Nairobi, Kenya, 18 October 2012

Published in: Technology, Business
  • I am a Young 27 years old PhD student in Plant Pathology at Haramaya University and conducting my research on ' Diversity of Aspergillus Species Associated to Groundnut (Arachis hypogaea L.), Levels of Aflatoxins and Management Options in Eastern Ethiopia'. I am suffering of research budget and I need for research fellow ship or grant for laboratory works for my laboratory works on molecular identifications of Aspergillus fungi and Aflatoxin analysis.
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BecA-ILRI Hub: Mobilizing biosciences for Africa’s development

  1. 1. Biosciences eastern and central Africa – International Livestock Research Institute (BecA-ILRI) Hub Mobilizing biosciences for Africa’s development Jagger Harvey BecA-ILRI Hub Nairobi, Kenya 18 October, 2012
  2. 2. Background AU/NEPAD – Africa Biosciences Initiative (ABI): Creation of four regional networks: 1. BecA (Biosciences eastern and central Africa) for countries in eastern and central Africa 2. SANBio (Southern African Network for Biosciences) for southern African countries 3. WABNet (West African Biosciences Network) consisting of ECOWAS countries 4. NABNet (North African Biosciences Network) for the countries in North Africa.
  3. 3. BecA countries BecA Nodes and other NARS • Ethiopian Institute of Agricultural Research, Ethiopia • Kigali Institute of Science and Technology, Rwanda • National Agricultural Research Organization, Uganda • Sokoine University of Agriculture, Tanzania • University of Buea, Cameroon • University of Nairobi, Kenya • Jomo Kenyatta University of Agriculture and Technology, Kenya • …and others BecA countries Burundi, Cameroon, Central Africa Republic, Congo Brazzaville, Democratic Republic of Congo, Equatorial Guinea, Eritrea, Ethiopia, Gabon, Kenya, Madagascar, Rwanda, São Tomé and Príncipe, Somalia, South Sudan, Sudan, Tanzania and Uganda.
  4. 4. 1. Research 2. Capacity building and training 3. Research and Technology-related services 4. Focal point for the agricultural research community in eastern and central Africa 5. Promotion of product development and delivery Core activities
  5. 5. BecA Hub Core competencies • Genomics/Metagenomics • Bioinformatics • Genetic engineering • Diagnostics • Molecular breeding • Vaccine technology/Immunology • Mycotoxins
  6. 6. Laboratory facilities for the Hub Capacity for over 300 users (>6000 m2) to provide for livestock, crop and microbial research and training.
  7. 7. Partners …and growing
  8. 8. Building a critical mass of scientists to tackle major agricultural issues Building a community of practice: • Core scientific and technical support staff • Scientists and technical staff from ILRI’s Biotech Theme, Sustainable Future Team • Scientists from other CGIAR centres (CIP, CIMMYT and IITA) • Affiliated prominent scientists located globally (e.g. Cornell University, Washington State University, Kenyatta University, University of Uppsala, etc.) • Africa, Australia, Europe, USA
  9. 9. Current major funding agreements 1. Syngenta Foundation for Sustainable Agriculture 2. AusAID through the BecA-CSIRO partnership is part of the Australia/Africa Food Security Initiative 3. The Bill & Melinda Gates Foundation core support to BecA-ILRI Hub 4. The Swedish Ministry of Foreign Affairs/SIDA 5. In addition to many other investors supporting our partners, graduate students, etc.
  10. 10. BecA-CSIRO partnership Capacity building through African Biosciences Challenge Fund • Courses and workshops • Visiting Scientists • Institutional Capacity Building Research Projects PPR ASF CBPP Mushrooms Amaranth Domestic cavies Animal Health R&D Food & Nutrition Science Core supportCo-investment and CSIRO/Australian scientific collaboration Aflatoxin
  11. 11. Swedish partnership Capacity building through African Biosciences Challenge Fund • Courses and workshops • Visiting Scientists • Institutional Capacity Building Research projects Core supportBioinformatics platform enhancement Staffing Harnessing genetic diversity for improving goat productivity in Africa Molecular diagnostics of crops and livestock diseases Tissue culture and plant transformation methods for addressing food security in Africa
  12. 12. BecA-SFSA partnership Capacity building •Workshops • •Technical support to Hub •Institutional Support •African Biosciences Challenge Fund (through salaries/core support) Emphasis Providing affordable access to African users, promoting African –led projects at Hub, and product development Core supportStaff salaries
  13. 13. BecA-BMGF Partnership Capacity building through African Biosciences Challenge Fund • Courses and workshops • Visiting Scientists • Institutional Capacity Building Key staffing/ core support • Genomics • Bioinformatics • Crop Breeding
  14. 14. Research
  15. 15. 1. Food safety  Mycotoxin 2. Nutritional security and income generation  Nutritional characterization and value addition of amaranth vegetable and grain by low cost sustainable processing  Domestication of wild edible mushroom species in Eastern Africa  Harnessing husbandry of domestic cavy for alternative and rapid access to food and income in Cameroon and the Democratic Republic of the Congo 3. Food security: crop and livestock improvement  Understanding the epidemiology of African swine fever (ASF) as a prerequisite for mitigation of disease impact on pig keeping in East Africa  Development of improved control interventions for peste des petits ruminants (PPR)  Providing proof of concept for the development of an inactivated vaccine for contagious bovine pleuropneumonia (CBPP)  Harnessing genetic diversity for improving livestock productivity: goats  Transgenic crops for disease and pest management  Maize-sorghum hybrid/molecular marker Major Research Programs
  16. 16. 4. Biosciences for climate change  Innovation programmatic approach to climate change in support of BecA-ILRI Hub’s mission: climate- smart Brachiara grasses for improving livestock production in East Africa  Biosciences for climate change adaptation 5. Disease diagnostics in crops and animals  Molecular diagnostics of crop and livestock diseases: adopting and adapting existing diagnostics to developing country laboratories 6. Agroecosystem health  African savannah grasses to generate new staple crop varieties and for rhizosphere management 7. Low science input: crops and animals (neglected crops and animals)  Tissue culture and virus indexing for production of virus-free planting materials in Africa Major Research Programs
  17. 17. Crop research support from hosted institutions
  18. 18. Research and technology services
  19. 19. Research related services at BecA Two core units • Sequencing genotyping and oligonucleotide (Segolip) unit • Central Core Unit (CCU) A state of the art genomics platform • Capillary Sequencing (ABI 3130, 3730 and 3500) • Next generation sequencing: Roche 454 pyrosequencer, MiSeq A state of the art bioinformatics platform • Genome assembly annotation, genotyping data analysis Mycology/mycotoxin and nutritional analysis platform • Near Infrared spectroscopy (NIR), Gas chromatography-mass spectroscopy (GC-MS), Ultra performance liquid chromatography (UPLC), Atomic absorption spectroscopy (AAS), Ultra violet-Visible (UV-VIS)
  20. 20. Segolip Unit: Current services Current Services a. DNA sequencing Sanger sequencing (capillary – low to medium throughput) Pyrosequencing (next generation – high throughput) b. Genotyping Full genotyping 01 (DNA extraction, PCR, fragment analysis) Full genotyping 02 (PCR, fragment analysis) Partial genotyping (fragment analysis) c. Oligonucleotides
  21. 21. BecA Genomics Platform Highlights of applications Genomics (microbial and other organisms) 1. Large genomes sequencing and re-sequencing 2. Viral genomics (African Swine Fever, Rift Valley Fever, blue tongue virus, equine encephalitis virus) 3. Functional genomics Metagenomics 1. Pathogen discovery, tracking and surveillance of zoonotic diseases (e.g. RVF) 2. Microbiome analysis; environmental metagenomics (e.g. aquatic environment)
  22. 22. The Bioinformatics Platform • High-performance computing server: – 32 total processing cores – 128GB of memory (RAM) – 8TB of disk space – 25TB LTO4 tape backup library • Linux cluster • 32 CPUs (AMD 64-bit) • 128 Gigabyte RAM • >10 terabytes disk storage • Grid computing • Parallel applications: > Genome assembly (Newbler, MIRA, Celera, velvet, CAP3. …) > Genome annotation (glimmer, …) > Phylogenetic analysis (Beast, Mr Bayes) > Other sequence analysis tools (BLAST, clustalw, HMMER, R)
  23. 23. Aflatoxin quantitation Screening for aflatoxin: ELISA test: semi-quantitative VICAM: AF total UPLC: AFB1, AFB2, AFG1, AFG2 and total Grinding: flour (sampling) Aflatoxin extraction Validations: ELISA-VICAM: R2 = 0.97 VICAM-UPLC: R2 = 0.99 ELISA-VICAM-UPLC: R2 = 0.98 Samples from field NIR scanning : calibration flour whole grain (ongoing) Culture and fungal identification: morphology, molecular and biochemical Mycology-Mycotoxin platform
  24. 24. Other Platforms Expanding our research, capacity building and service opportunities 1. Diagnostics platform (from sequence to impact): Animal and crop diseases 2. Online data integration and analysis platforms 3. Mobile-based data collection and delivery system using Google's app engine
  25. 25. Capacity building … and more
  26. 26. Capacity Building Objectives • Strengthen capacity of individuals and institutions to harness the latest biosciences technologies to improve agriculture in Africa • Support African scientists efforts to lead and sustain biosciences research in Africa • Promote access to world-class research and training facilities at the BecA–ILRI Hub
  27. 27. Capacity building activities 1. Research placements: ABCF and independent placement • Graduate students • Visiting scientists 2. Training workshops (annual and ad hoc) 3. Conferences 4. Institutional capacity building 5. Linkages, information, creating awareness of the BecA-ILRI Hub
  28. 28. The African Biosciences Challenge Fund: Building African science leaders • A competitive fund which enables scientists to progress research at biosciences “centre of excellence” = BecA-ILRI Hub • Open to scientists and students from African national research institutes and universities • Mentoring and support, training workshops • 50 + placements available annually • Growing support of various donors
  29. 29. Training workshops • Annual practical training workshops organised by BecA-ILRI Hub i. Introductory molecular biology and bioinformatics ii. Advanced bioinformatics and genomics iii. Laboratory management & equipment maintenance iv. Science paper writing
  30. 30. Product development, incubation and delivery
  31. 31. Product development, incubation and delivery • Passion fruit virus diagnostics • Virus-free taro plant materials: diagnostics and tissue culture methods (Burundi and Ethiopia) • PPR thermostable vaccine in Sudan • New molecular tools to study theileria diversity • East Coast fever: rapid sero-diagnostics (to be transferred to labs with very limited facilities)
  32. 32. The BecA Hub team 09 countries Australia, Benin, Cameroon, England, Ethiopia, Italy, Kenya, Scotland, USA
  33. 33. Acknowledgements • The Government of Kenya • Canadian International Development Agency (CIDA) • Syngenta Foundation for Sustainable Agriculture • AusAID/CSIRO • The Bill & Melinda Gates Foundation • Swedish Ministry for Foreign Affairs • SIDA • Roche • Rockefeller Foundation • Gatsby Charitable Foundation • Doyle Foundation • UNESCO • IFS • Many others