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
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.
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.
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
BecA Hub Core competencies
• Genomics/Metagenomics
• Bioinformatics
• Genetic engineering
• Diagnostics
• Molecular breeding
• Vaccine technology/Immunology
• Mycotoxins
Laboratory facilities for the Hub Capacity for over 300 users
(>6000 m2) to provide for livestock, crop and microbial research and training.
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
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.
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 support Co-investment and CSIRO/Australian scientific collaboration
Aflatoxin
Swedish partnership
Capacity building through
African Biosciences Challenge Fund
• Courses and workshops • Visiting Scientists • Institutional Capacity
Building
Research projects
Core support Bioinformatics 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
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 support Staff salaries
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
Research
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
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
Crop research support from hosted institutions
Research and technology services
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)
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
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)
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)
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
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
Capacity building
… and more
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
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
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
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
Product development, incubation and delivery
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)
The BecA Hub team 09 countries Australia, Benin, Cameroon, England, Ethiopia, Italy, Kenya, Scotland, USA
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
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