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

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. 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. 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. 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. BecA Hub Core competencies
• Genomics/Metagenomics
• Bioinformatics
• Genetic engineering
• Diagnostics
• Molecular breeding
• Vaccine technology/Immunology
• Mycotoxins

6. Laboratory facilities for the Hub
Capacity for over 300 users
(>6000 m2) to provide for livestock,
crop and microbial research and
training.

7. Partners
…and growing

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. 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. 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. 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. 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. 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. Research

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. 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. Crop research support from hosted institutions

18. Research and technology services

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. 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. 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. 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. 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. 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. Capacity building
… and more

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. 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. 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. 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. Product development,
incubation and delivery

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. The BecA Hub team
09 countries Australia, Benin, Cameroon, England, Ethiopia, Italy, Kenya, Scotland, USA

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