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

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.

Partners

…and growing

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