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These projects were identified through a series of workshops including African and Australian and other partners, focused on food and nut sec
BecA hub research, facilities, and capacity building
Biosciences eastern and central Africa (BecA)Biosciences eastern & central Africa (BecA) HubInternational Livestock Research Institute (ILRI), Nairobi, Kenya
BecA Hub: Core activities1. Research Core competencies and research programs in agriculture: crop, animal health and microbial sciences2. Capacity building and training3. Research and Technology-related services4. Focal point for the agricultural research community in eastern and central Africa5. Promotion of product development and delivery
Laboratory facilities for the HubSeven laboratories to provide for livestock, crop and microbialresearch and training.Laboratory upgrade and construction:
Partnerships 2011 2010 2009 2008 2007 2006 2005 18(+) supported countries: Universities Nat’l Ag Research Systems (NARS) 2004 Research Institutions Nodes: University of Buea, Cameroon2003 Ethiopian Institute of Agricultural Research Sokoine University of Agriculture, Tanzania National Agricultural Research Rural Development Organization, Uganda Administration of the Republic of Korea and more… Kigali Institute of Technology, Rwanda
Current BecA Hub Major Funding Agreements• Syngenta Foundation for Sustainable Agriculture (USD 5M; 2009-14)• The BecA-CSIRO partnership is part of the Australia/Africa Food Security Initiative (AUD$ 14M; 2009-13): AusAID• The Bill & Melinda Gates Foundation core support to BecA Hub (USD 2M, 2011-14)• The Swedish Ministry of Foreign Affairs/SIDA (USD12M, 2012- 2015)• In addition to many other investors supporting our partners, graduate students, etc.
SFSA Partnership SFSA BecA Hub Staff salaries Core support Emphasis: Capacity building providing affordable Workshopsaccess to African users, Technical support to Hubpromoting African –led Institutional Support projects at Hub, and African Biosciences product development Challenge Fund (through salaries/core support)
BecA-CSIRO Partnership AusAID CSIRO BecA Hub Research Projects Capacity building through African Biosciences Animal health R&D PPR Aflatoxin Amaranth Challenge Fund ASF Food & Nutrition Science • Courses and workshops Mushrooms Domestic • Visiting Scientists CBPP cavies • Institutional Capacity BuildingCSIRO/Australian scientific collaboration, co-investment and partnership management Core support
BMGF Partnership BMGF BecA Hub Capacity building Key staffing/ through African Biosciences core support Challenge Fund Genomics • Courses and Bioinformatics workshops Crop Breeding • Visiting Scientists • Institutional Capacity Building
Swedish Partnership Ministry for Foreign Affairs SIDA BecA Hub Research Projects Capacity building through Goat improvement African Biosciences Molecular diagnostics: crop and animal diseases Challenge Fund • Courses and Plant tissue culture & virus indexing workshops • Visiting Scientists staffing • Institutional Capacity Building Bioinformatics Core support platform enhancement
CAAREA: Activities to dateCapacity and Action for Aflatoxin Reduction in Eastern Africa (CAAREA)
Aflatoxin research – critical gapsPotential Intervention Points:Pre-harvest: varieties (eg, KARI 170 to date)Insect damage/resistanceBiocontrolDryingStorageBinding clay
Capacity and Action for Aflatoxin Reduction in Eastern Africa (CAAREA)CAAREA objectives1. Establish mycotoxin diagnostics platform at BecA2. Characterize Aspergillus flavus from around Kenya and Tanzania (maize and soil): as source of inoculum, resolve key population biology/pathosystem questions, etc.3. Test modeling as a potential predictive tool and to contextualize findings across Kenya, Tanzania and the region.4. Identify maize germplasm resistant to aflatoxin accumulation in specific environments (field trials and postharvest experiments), including GxE(xM).5. National breeders leading field trials will affect subsequent changes to Kenyan and Tanzanian maize breeding programs.
Capacity and Action for Aflatoxin Reduction in Eastern Africa (CAAREA)Projected impact:In Kenya alone, it is estimated that over 5.6 million people in drought prone areas inEastern and coastal lowlands alone will directly benefit from maize varieties with reducedmycotoxin accumulation.In Tanzania, not only does maize provide 60% of daily dietary calories and about 50% ofprotein, but it is also a cash crop for 85% of the current Tanzania’s the population which isestimated at about 41 million.Platform will extend the impact by enhancing capacity to address mycotoxins in theregion.
CAAREA partnersKenya:BecA Hub at ILRI: Jagger Harvey (Project Leader, Research Scientist); Benoit Gnonlonfin (postdoc); Samuel Mutiga (Cornell PhD student); Eric Magembe; Vincent WereKARI: James Gethi and team, National Maize Research CoordinatorUniversity of Nairobi: Sheila OkothTanzania:ARI: Arnold Mushongi, National Maize BreederOpen University of Tanzania: Said MassomoAustralia:Ross Darnell, biometrician, CSIROMary Fletcher, natural product organic chemist, QAAFI/Univ. QueenslandGlen Fox, NIR expert, QAAFI/Univ. QueenslandDarren Kriticos, ecological modeler, affiliated with CSIRO and Harvest ChoiceUSA:Rebecca Nelson, Cornell UniversityMichael Milgroom, Cornell UniversityPhil Pardey, University of Minnesota, Harvest ChoiceOther linked scientists:Yash Chauhan, DEEDI (APSIM modeling for predicting aflatoxin risk)Stephen Trowell, CSIRO (electronic nose development as a potential aflatoxindetection method)
Harnessing husbandry of domestic cavies for alternative and rapid access to food and income (Cameroon and Eastern DRC)Justification: Domestic cavies and other short cycle alternative livestock have great potential to contribute to addressing food security challenges in developing countries.Objectives:1. Characterize current production systems & establish cavies production innovation platforms.2. Generate and integrate genetic diversity data with other breeding information to design a sustainable cavies production system.3. Improved feed system for higher cavies productivity.4. Information dissemination and capacity building.Partners:ILRI/BecA Hub: Appolinaire Djikeng (PI), Mwai Okeyo, Francis WamonjeCIAT (International Center for Tropical Agriculture)Cameroon: University of Dschang and Min of Livestock, Heifer Prog International, Farmers’ VoiceDRC: Universite Evangelique en Afrique, Women for womenAustralia: CSIROPathway to impact: Improved husbandry practices will be disseminated for a sustainable caviesproduction linked to market and consumption.
Domestication of wild edible mushrooms in E. Africa (Nat’l Program-Led)Justification: Income generation.Objectives:1. Collect and characterize wild edible mushrooms.2. Domesticate them on agro-wastes (eg, sisal, rice straw).3. Nutritionally profile domesticated varieties.4. Farmer training.Partners:University of Dar es Salaam Prof. Amelia Kivaisi (PI)Kenya Industrial Research andDevelopment Institute (KIRDI)University of BurundiCSIROBecA Hub at ILRIPathway to impact:Existing mushroom domestication and training programs at each institution will be expandedto include these indigenous varieties.
Amaranth (Nat’l Program Led)Justification: Amaranth is popular (vegetable & grain) in many African countries.Objective:Reduce food and nutrition insecurity in rural communities of SSA by increasing amaranthproduction & transforming its leaves and grain products into a variety of shelf stable,nutritious, highly acceptable and marketable products.Partners:Jomo Kenyatta University of Agriculture and Technology Dr Daniel Sila (PI)Sokoine University ofAVRDC (Tanzania)CSIROBecA Hub at ILRIPathway to impact:Stakeholder consultations & training through established extension activities at the Africaninstitutions will be used. Amaranth is very popular in these countries.
PPR Development of Improved Control Interventions for Peste des Petits Ruminants (PPR)Justification: PPR is an important disease of small ruminants with challenges in vaccine delivery (cold chain,…).Objectives:1: To thermostabilize existing PPR vaccine Nigeria 75/1 strain - OIE recommended Widely used in Africa2: To pilot vaccine delivery modelsPartners:BecA-ILRI BiotechAu-IBARAustraliaPathway to impact:Research embedded in development (ILRI and AU-IBAR) and piloting of vaccination/newinstitutional models will help ensure delivery of an improved vaccine.
The BecA Hub:A key driver for Agricultural transformation LOCATION: well positioned to co-operate with regional and international partners. CAPACITY: build a critical mass of scientists by training and engaging them in a wide range of research activities. SCIENCE: focused on research that can address pressing constraints for Africa’s smallholder farmers.
Research-related services at the BecA Hub and their impact on research and capacity building
BecA Hub: Core activities1. Research2. Research-related services3. Capacity building and training4. Focal point for the agricultural research community in eastern and central Africa5. Promotion of product development and delivery
Presentation outlineI. The Central Core UnitII. The SEGOLIP UnitIII. The Genomics platformIV. The Bioinformatics platformV. Other platforms
I. Central Core UnitStaff (10)• 01 Manager• 03 Tech Lab Ass• 06 Lab cleanersCurrent services• Laboratory cleaning and waste management• Glassware cleaning and sterilization services• Preparation of culture media and buffers• Mol Biol grade water, custom made solutions
I. Central Core Unit (Cont’d)Users/customers• BecA Hub staff and all African researchers using the Hub• ILRI Biotech (media/buffers and packaging of the ITM vaccine)• Hosted institutions (IITA, CIMMYT, CIP)• Kenya Agricultural Research Institute (KARI)• Kenya Medical Research Institute (KEMRI)• Institute for Primate Research (IPR)• Universities (Univ of Nairobi, JKUAT, KU, MMU, Egerton Univ)• icipe• Other CG centers based in Nairobi• Syngenta Flowers• Makerere University, Uganda• MARI, Tanzania
I. Central Core Unit (outlook)Expansion to other users/customers)• Other institutions in the region (Hub activities’ expansion)Other services under consideration (include)• Molecular biology reagents (nucleic acids extraction reagents, DNA size standards)• Enzymes (i.e. Taq DNA polymerase)
II. SEGOLIP UnitStaff04 technical staffExtensive lab experienceCurrent Servicesa. DNA sequencing Sanger sequencing (capillary – low to mediumthroughput) Pyrosequencing (next generation – high throughput)b. Genotyping Full genotyping 01 (DNA extraction, PCR, fragmentanalysis) Full genotyping 02 (PCR, fragment analysis) Partial genotyping (fragment analysis)
II. SEGOLIP Unit (Cont’d) Supporting a wide range of research projects Banana Beans Arthropod Cassava vectors Cowpea Buffalo Eucalyptus Chicken Maize Cow Millets GoatNapier grass Pigs Ocimum SheepPassion fruit Mice Pigeon pea Wildlife Rice Sorghum Striga Bacteria Sugar cane FungiSweet potato Parasites Tef Viruses Yam
II. SEGOLIP Unit (Cont’d) Supporting a wide range of programs1. Generation Challenge Program (GCP): 2011 Work Order• 09 countries (South Africa, The Philippines, Kenya, Ghana, Ethiopia, Uganda, India, Burkina Faso, Mexico)• 10 crops (maize, rice, sorghum, cowpea, chickpeas, cassava, sweet potatoes, beans, finger millet, pearl millet)2. Projects at the Hub facilities• Support (services and training) to all ABCF fellows, AWARD fellows, graduates students and other visiting scientists projects• ILRI Biotech Theme• Hosted CGIAR crop centers3. Other users (African NARS, universities, international research institutesand regional programs, USA, Latin America, Middle East and Asia)
II. SEGOLIP Unit (Cont’d) supporting various breeding programs in Africa1. Characterization of sorghum germplasm collection focusing on biotic andabiotic stresses (Kassahun Bante – Jimma University, Ethiopia)2. Stress Tolerant Rice for Africa and South Asia (STRASA) project: Developmentand delivery of improved rice varieties that are tolerant to five major abioticstresses; drought, submergence, salinity, iron toxicity and low temperature(Negussie Zena – Africa Rice Center)3. Cassava breeding in Uganda (Robert Kawuki, NARO, Uganda)4. Genotyping of sorghum BC4F1 population associated with striga resistance(Rasha Ali – University of Khartoum, Sudan)5. Genetic diversity to support a goat breeding program in Cameroon (FelixMeutchieye – University of Dschang, Cameroon)6. Genetic characterization of Senegalese trypanotolerant N’Dama cattle (MameDiouf – ISRA, Senegal)
II. SEGOLIP Unit (Cont’d) A steadily increasing demand DNA SEQUENCING SERVICE PER YEAR 8000 7000 6000 5000No of Samples 4000 * 3000 2000 1000 0 2005 2006 2007 2008 2009 2010 2011 Year
Su # Full genotyping 01 ga rI nd us # Data 2010 – Aug 2011 tr yR es ea rc h Bi In Ke ot s Un ny ec tu ive a hn te 0 100 200 300 400 500 600 700 rs Fo ol (M ity re og au of st r yC ri Fr yR en us ee sta es ea te r( ) te rc Ec h ua Number of Samples -B In lo em s do r) tu fo te Un nt (K ive ein en rs (S ya ity ou ) of th Un Kw Af Af ive a- ric ric rsi zu aR a) ty lu i ce of Na Ce Ca ta nt lif l( er or So ni ut a- hNa Un Lo Af ric on ive sA ng a) al rs Cr ity ele op of s( Re Jim Zim US so m ba A) ur aU bw ce s ni ve e( Re rsi ZW se ty ) Ke ar (E ch th ny In io aA Eg s pi Na gr er tu a) icu to te n (U serving institutions within and out of Africa on ltu Institutions using genotyping services al ra Un ga Ro lR ive nd ot es rs a) Cr ea ity op rc (K h en sR In es s ya ea tu ) rc te h (K In en s ya tu ) te (N ige ria )
IV. The Genomics platform Opportunities for genomics and metagenomics research ABI 3130-xl ABI 3730-xl ABI 3500-xlCapillary sequencing 1 sample = 1 library = 1 plate Next generation 500 mb/run sequencing: 1/2 cassava genome 1/8 human genome454 GS pyrosequencer
IV. The Genomics platform (Cont’d) Highlights of applicationsGenomics (microbial and other organisms)1. Large genomes re-sequencing (Cassava)2. Viral genomics (African Swine Fever, Rift Valley Fever, blue tongue virus, equine encephalitis virus)3. Functional genomics (small viral RNAs in cassava)Metagenomics1. Pathogen discovery, tracking and surveillance of zoonotic diseases (e.g. RVF)2. Microbiome analysis; environmental metagenomics (e.g. aquatic environment)
IV. The Genomics platform (Cont’d) Major outputsCompleted and ongoing projects1. Re-sequencing of the cassava genome # 06 next gen sequencing runs => 1.4 billions bases => ~ 1.5x coverage of the cassava genome # Ongoing data analysis (BecA Hub/IITA, Univ Arizona)2. Deep sequencing to support a study on soil management (Study on the interaction between resident and inoculated mycorrhizal communities) – TSBF-CIAT # ¼ next gen sequencing run with 36 multiplexed samples # Ongoing data analysis (BecA Hub, TSBF-CIAT)
IV. The Genomics platform (Cont’d) Major outputs3. Pathogens genomes sequencing projects (61 viral genomes sequenced so far with 14 deposited @ Genbank) # Rift valley fever virus (16 sequenced and ongoing analysis) # New castle disease virus (03 sequenced and deposited @ Genbank) # African swine fever virus (02 sequenced and ongoing analysis) # Equine encephalitis virus (05 sequenced and ongoing analysis) # Blue tongue virus; collection 1970 – now (24; ongoing sequencing) # Ndumu Virus (07 partially sequenced) // also found in pigs (discovery !!) # Other viruses: Dugbe virus (01), semliki virus (02), bunyamwera (01); deposited @ Genbank
V. The Genomics platform (Cont’d) Highlights of forthcoming projectsGenomics:# Genome sequencing of napier stunt disease pathogen, phytoplasma (icipe, ILRI)# Genomics of Novel Respiratory Adenovirus isolates (CDC, Kenya)# Genomic characterization of hMPV isolates in of Kenya (Walter Reed, Kenya)# Heredity and Human Health in Africa (H3 Africa – sequencing and genotypingsupport), Wellcome Trust and NIH# Development of new markers (Enset, etc..)Metagenomics:# Microbial community in selected environments of Nairobi city district (Univ NotreDame, ILRI)# “Viromes” of selected African farming systems; assessing food security risks(BecA, KARI, FERA)# Heredity and Human Health in Africa (H3 Africa – sequencing support)
IV. The Bioinformatics platform• 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 IRRI – Philippines BecA/ILRI Bayes) ICRISAT – India > Other sequence analysis tools CIP – Peru (BLAST, clustalw, HMMER, R) Bioinformatics Group Leader Dr Etienne de Villiers
IV. The Bioinformatics platform (Cont’d) Selected outputs1. Research support # Genomics approach to the identification of virulence genes of CBPP # Genomics approach to the development of vaccines and diagnostics of camel Streptococcus agalactiae (to support camel milk marketing through improved control of mastitis) # Cassava genome project # Molecular markers development # Diagnostic development (ex. Passion fruit)2. Capacity building # Since 2006: 15 bioinformatics courses (~ 391 participants from African institutions) # Established a Regional Student Group (RSG) affiliated with The International Society for Computational Biology (ISCB) in 2007
VI. Other platforms Expanding our research and capacity building and services opportunities1. Diagnostics platform (from sequence to impact): exploiting genomic data Animal and zoonotic diseases Crop pathogens: Viral diseases Bacteria Ralstonia solanacearum (Endemic disease - keep this out of local seed) Dickeya solani (European disease - keep this out of the region)
VI. Other platforms Expanding our research and capacity building and services opportunities2. Mycotoxin and nutrition analysis platform Infrastructure: Atomic Absorption Spectrophotometer Gas chromatograph – Mass Spectrophotometer (GC-MS) HPLC system comprising UHPLC solvent system Fourier Transform Near Infrared (FT-NIR) spectrometer Applications/measurements: Mycotoxins, sugars, vitamins, carotenoids, phenolics, fatty acids and amino acids, trait analysis (crops and animals)
VI. Other platforms (Cont’d) Expanding our research, capacity building and service opportunities3. Online data integration and analysis platforms iPlant Collaborative (Cyberinfrastructure to support plant biology research. # Sustainable access to high performance computing, interoperable software analysis, and large data sets ibp (Integrated breeding platform: public web-based one-stop shop for information, analytical tools and related services to design and efficiently conduct molecular-assisted breeding experiments)
Strategies for new equipment and technologies acquisition
Strategies for new equipment and technologies acquisition (Some challenges!!!) BecA Hub Lab asset distribution >100K (30%) 5OK-100K (10%) 10K - 50K (30%) < 10K (30%)Equipment replacement plan # < 100 000 USD (Grants) # > 100 000 USD (special donations) # Capital expenditure ???
Thank youBiosciences eastern & central Africa (BecA) HubInternational Livestock Research Institute (ILRI), Nairobi, Kenyahttp://hub.africabiosciences.org
“Biosciences are seen as one of the major engines of growth in the world in fields such as …. agriculture. Africa lags behind in biosciences. The two key problems are lack of sufficient funding from governments and shortage of skilled expertise.” NEPAD www.nepad.org/humancapitaldevelopment/abi
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 Hub
Building biosciences capacity for improving African agriculture 1. Research placements • Graduate students • Visiting scientists 2. Individual/small group training 3. Training workshops 4. Conferences 5. Institutional capacity building 6. Linkages, information, creating awareness of BecA Hub
Growing numbers using the HubGraduate students, visiting scientists and short term trainees
Individual/small group training• 1-5 trainees• 1-4 weeks• Customised training• One or more technologies
Training workshops• Hosted by the BecA Hub – 2007-2011: 42 training workshops – Examples (2011): • Basic Laboratory Health and Safety (ILRI, BecA) • Marker Assisted Breeding (ICRISAT)• Annual practical training workshops organised by BecA Hub, under ABCF 1. Science paper writing 2. Introduction to molecular biology and bioinformatics 3. Advanced bioinformatics 4. New for 2012: Laboratory management & equipment maintenance
Science Writing Workshops: 2009 - 2011• Applications: 703 (2009), 560 (2011)• 64 participants from 15 African countries (27 women,37 men)• Outputs (2009, 2010): 24 papers submitted, 15published• 2009: BMGF funding; training by Scriptoria• 2010, 2011: AusAID funding; training led by CSIRO “I had been struggling for one year with my introduction, but I finished it in one afternoon.” Anne Akol, Senior Lecturer, Makerere University, Uganda
Molecular Biology and Bioinformatics Workshop 2011• 21 participants (6 women, 15 men)• 10 African countries• Research discovery process Tissue DNA PCR Cloning Sequencing BLAST Sequence analysis
Advanced bioinformatics workshop 2011: Next Generation Sequencing for Africa• 24 participants (18 men, 6 women) from Africa• 13 tutors from Kenya, Europe, USA• EMBO Global Exchange Lecture Course: Next Generation Sequencing data analysis• 4 collaborations initiated - RVFV (VRI-Sudan, ILRI-BecA) - Finger millet SNPs (KU-Ke, U Liverpool) - Trypanosome MDR (SUA-Tz, U Liverpool) - Drought stress in banana (Makerere U-Ug, BecA)
Building capacity through research• Major focus – Post graduate research projects (up to 3-4 yrs) – Students registered at many universities – Visiting scientist placements (up to 6 months) – Employees from NARIs and UniversitiesABCF: African Biosciences Challenge Fund
Making the ABCF possible• Syngenta Foundation for Sustainable Agriculture (SFSA)• BecA-CSIRO partnership funded by the Australian Agency for International Development (AusAID)• The Bill & Melinda Gates Foundation (BMGF)• Ministry for Foreign Affairs, Sweden, through the Swedish International Development Cooperation Agency (SIDA)
ABCF Research Fellowships• Large demand for use of BecA Hub: inadequate funds• Enable African scientists access Hub facilities and services, for high quality research addressing African agricultural problems• Researchers from national research institutes and African universities• 3-6 months at the Hub• Competitive basis or targeted ‘fast track’
ABCF Research FellowsCharles MasembeDepartment of Zoology, Makerere University, UgandaPig diseases and food security: Next-generation DNAsequencing of African swine fever virus (ASFV) in UgandaSelamawit Bedane (Haramaya University, Ethiopia)Sisay Alemu (Holetta Agricultural Research Center, EIAR, Ethiopia)Molecular characterization of enset from Ethiopia usingbanana microsatellite markers
ABCF Research FellowsDia HassanCentral Veterinary Research Laboratories, Khartoum, SudanTheileria parva genotyping to support control of East Coastfever, an emerging disease in South Sudan Dora Kilalo Department of Plant Science and Crop Protection, University of Nairobi Passion fruit woodiness disease diagnostics
ABCF Research FellowsAlexander BombomDepartment of Agricultural Production, Makerere UniversityMolecular characterization of maize-sorghum hybrids Félix Meutchieye University of Dschang, Cameroon Molecular characterization of Cameroon indigenous goats and sheep
Building capacity of African institutes• National Agricultural Biotechnology Centre, Holetta, Ethiopia• Gulu University, Uganda• Mikocheni Agricultural Research Institute (MARI), Tanzania
Raising awareness38 institutes and organisations in 8 countries visited in 2011 • Burundi • Cameroon • Ethiopia • Rwanda • Sudan • Tanzania • Uganda • Nigeria • Conferences in many countries • BecA workshops • Website • Printed materials • We host over 1500 visitors per year
Integration of research, capacity building and research- related services For a better delivery of the BecA mission Research Research Capacity related building services
Acknowledgements• Australian Agency for International Development (AusAID)/CSIRO• Bill & Melinda Gates Foundation (BMGF)• Ministry for Foreign Affairs, Sweden, through the Swedish International Development Cooperation Agency (SIDA)• Syngenta Foundation for Sustainable Agriculture (SFSA)• NEPAD/AU• Canadian International Development Agency (CIDA)• Google Foundation• Rockefeller Foundation• Gatsby Charitable Foundation• Doyle Foundation• The Kenyan Government• and many others