Building African bioinformatics skills and expertise locally

Specialists at a new-age computing facility are seeking partnerships with international universities to develop world-class bioinformatics capacity in Africa – and Africa's first generation of bioinformaticians.
One of the great recent successes of African biosciences was mapping the genetic code of a parasite known as Theileria parva. This single-celled parasite is transmitted to cattle by biting ticks and causes East Coast fever, which kills a million cattle a year in 11 countries of Africa and is responsible for up to half of all deaths of calves kept by pastoralists there. Much of the work that contributed to this world-class scientific breakthrough, published in the prestigious journal Science, was undertaken in Africa by scientists at the International Livestock Research Institute (ILRI), in Nairobi, Kenya, in partnership with scientists at The Institute for Genomic Research (TIGR), based in the Maryland, USA.

Working with ILRI, scientists at TIGR first sequenced the genome of the T. parva parasite. Most of the subsequent work in annotating the sequence by identifying genes and assigning gene functions was performed by two bioinformatics specialists at ILRI— South African Etienne de Villiers and Kenyan Trushar Shah—using ILRI’s new high-performance computing facility at its Nairobi laboratories.

de Villiers, Shah and colleagues are hoping to build on this breakthrough to strengthen bioinformatics capacity in Africa. They are forming partnerships with leading universities worldwide with the aim of offering post- and under-graduate training in bioinformatics in and for Africa until African universities begin offering masters and doctoral degrees in this new discipline.

Genomics is the molecular characterization of all the genes in a species. It is concerned with sequencing and mapping all of the genes—together known as the genome—that make up a given species, and from this information, establishing what makes the species and the individuals within the species unique. Those working in genomics are interested to discover, for example, how genetic make up is responsible for making some species and individuals susceptible to disease while otheres tolerate or resist the same disease. The prospect of discovering such important biological factors makes genomics one of the most exciting fields in science today. Developments are rapid and new insights are being gained daily.

Bioinformatics is a combination of computer, information and biological sciences. Bioinformatics takes advantage of new computing and information technologies and exploits these to help scientists answer complex biological questions. Specialist databases and tools are used to manage the huge amounts of complex biological data being generated by genomics.

 High-performance computing in and for Africa
The high-performance computing facility on ILRI’s campus in Nairobi provides local scientists with access to state-of-the-art technologies to enable them to conduct extensive and large-scale genomics research fast and cost-effectively for the first time. The facility has been established in Nairobi to serve the bioinformatics needs of ILRI and the eastern and central African scientific community. It is being managed as a shared facility by a new regional science platform called ‘Biosciences eastern and central Africa’ (BecA), whose hub is at ILRI’s Nairobi laboratories.

Etienne de Villiers explains that, ‘Exploitation of the latest genome technologies requires scientists skilled in bioinformatics and with access to high-performance computing infrastructure. The strategy behind high-performance computing is “divide and conquer”. Dividing a complex problem into smaller component tasks, that can be worked on simultaneously by computer, saves time, physical and human resources and money.

‘Bioinformatics is a relatively new specialist area. We need to raise awareness of the field here in Africa and expose people to its potential. The West has spent millions of dollars sequencing the genomes of humans, animals, plants and parasites and the resulting data are freely available on the internet. This is a vast body of knowledge that local scientists can use to solve their specific problems or to answer research questions. All scientists in Africa need to make use of these data are a computer, good internet access and bioinformatics skills.’

Raising awareness and building capacity in Africa
ILRI/BecA training courses and research projects are already taking advantage of the high-performance computing facility, which was commissioned in January 2005. In association with the Swedish University of Agricultural Sciences and the Linnaeus Centre for Bioinformatics, in Uppsala, Sweden, ILRI and BecA recently ran a three-day training workshop that introduced 30 scientists and students from eastern and central Africa to the field of bioinformatics.

BecA scientist Trushar Shah says that ‘bioinformatics is a new and dynamic field that young African scientists should be getting involved in, whether as a specialist or a user exploiting the technology to help answer a complex research question. Our recent short training course was very successful and we are organizing a further course in April 2007.’


African bioinformatics skills and expertise

Participants at the Bioinformatics introductory course, August 2006

Home grown strategies and interim partnerships
de Villiers is an advocate of home-grown strategies that take into consideration local needs to build capacity in Africa. ‘One of our primary goals is to grow the number and competence of bioinformatics developers and users in the east and central Africa region. To do that, we have to be responsive to local needs. We are raising awareness of the importance and utility of bioinformatics, providing introductory training for early-career scientists, and giving skilled bioinformaticians in the region ready access to advanced tools, support and expertise. We are also considering the longer term and how best we can contribute to building bioinformatics skills and expertise throughout Africa.

‘Local universities are working hard to build capacity but at the moment are unable to award degrees in bioinformatics. Our thrust now is to explore partnerships with leading bioinformatics institutes to enable us to make undergraduate and postgraduate training possible. We are working to link up with universities with well-established training programs in bioinformatics to offer East and Central African students masters and doctoral degree training in bioinformatics, possibly through distance learning.
‘We are also planning to link up with universities and institutes that can host these students for a few months so they can gain practical experience in the applications of bioinformatics. This way we are also training future local trainers.’

de Villiers was recently made Extraordinary Lecturer at the Bioinformatics and Computational Biology Unit of Pretoria University, in South Africa. This appointment enables him to supervise students from eastern and central Africa who are affiliated with the high-performance computing facility and wish to pursue higher degrees in bioinformatics through Pretoria University.

ILRI vaccine advances published in February 2006 PNAS journal

Public-private partnership makes major step towards improving livestock health and reducing poverty.

The devastating effects of East Coast fever on the livelihoods of small-scale farmers may one day be a thing of the past as a team of international scientists moves closer towards the development of a vaccine.

“East Coast fever is an intractable problem that ravages cattle of the poor in Africa. The good news is that this can be solved by high-tech science and technological innovations, achievable through strategic partnerships’’. Evans Taracha – ILRI East Coast Fever Vaccine Project Leader

Every year, East Coast fever destroys the small farmer’s dream of escaping poverty in Africa. Killing more than a million cattle and costing some $200 million annually, this tick-borne disease rages across a dozen countries in eastern and central Africa. Now, an international team of scientists has taken the first major step toward a vaccine to prevent East Coast fever. Their work, published in the February 13-17 early online edition of the Proceedings of the National Academy of Sciences (PNAS), shows how genomics can generate pivotal new vaccines.

In the study, scientists from five institutions, including the International Livestock Research Institute (ILRI) and The Institute for Genomic Research (TIGR), identify five vaccine targets, or candidate proteins that could form the basis for an East Coast fever subunit vaccine. Based on combined bioinformatics analyses and lab tests, these proteins appear to provide a protective immune response to the disease. “This initiative took just three years, after many years of scientists trying other methods,” remarks Vishvanath Nene, former ILRI staff member, a study author and molecular biologist at TIGR. “It’s a huge jump forward.”

To make the jump, researchers used the genome sequence of the parasite responsible for East Coast fever. A tick-borne parasite, Theileria parva, causes the disease. When ticks infected with T. parva bite cattle, they transmit the parasite, launching the disease that typically kills cattle within a month. In July, 2005, TIGR led a research team that published T. parva’s genome sequence, representing roughly 4,000 genes, in Science.

In the current study, Nene, along with Malcolm Gardner and Claire Fraser-Liggett, also of TIGR, relied on known biology to search T. parva’s genome for potential vaccine proteins. First, scientists know that immunity to the parasite, and thus East Coast fever, emerges from immune system cells known as killer T cells. Second, they know that T. parva is an intracellular pathogen–it infects and secretes proteins inside cattle white blood cells, which become malignant. The white blood cell then unwittingly passes small fragments of the secreted parasitic proteins associated with a certain type if its own proteins along to its cell surface. And this is where a vaccine could come in: A vaccine made of the T. parva proteins found on the surface of host cells should trigger an immune response in cattle. Vaccinated cattle would then be protected from the parasite.

To find potential vaccine antigens, the TIGR researchers scanned T. parva’s entire genome for genes that make secreted proteins. In particular, they searched for genes that make a “secretion signal,” a telltale peptide sequence found at the start of secreted proteins. Sure enough, the scientists found some 400 T. parva genes containing the secretion signal. This set of genes provided a starting pool of candidate proteins. Based on further tests, the study’s research team, led by ILRI of Nairobi, Kenya, cloned 55 candidate antigen genes and screened those genes for response by killer T cells taken from cattle immune to East Coast fever. To complement TIGR’s gene selection strategy, ILRI also incorporated a random screen of T. parva DNA for vaccine candidates.

In total, the team found five candidate vaccine antigens. In lab tests, these antigens triggered a response from cattle immune killer T cells. Going a further step further, the scientists inoculated cattle with these antigens and then gave the cattle a potentially lethal dose of T. parva. When compared with control animals, vaccinated cattle showed significantly stronger immune response to the parasite.

“This study is a true milestone,” says Fraser-Liggett, president of TIGR. “It’s one of the first to take advantage of genomic technologies and build a test vaccine using immune killer T cells as a screening reagent.” In addition to TIGR and ILRI, the research team included scientists from: the Ludwig Institute for Cancer Research in Brussels; the Wellcome Trust Center for Human Genetics in Oxford; Sanofi Pasteur in Toronto; the University of Edinburgh; and Merial SAS, an international animal health company. ILRI and Merial have partnered to develop a vaccine against East Coast fever.

By using genomics to understand and fight T. parva, scientists may make advances against related parasites that cause malaria, tuberculosis, and other diseases in which killer T cells also play a role in immunity. What’s more, because T. parva launches a cancer-like illness inside the white blood cells of cattle, it may provide a model system for understanding the mechanics of cancer biology.

But for Nene, who was born in Kenya and worked at ILRI for 15 years before coming to TIGR in 2001, the march against East Coast fever is significant reward, itself. “This disease takes an enormous toll on the local society and economy of rural areas across eastern and central Africa, including Maasai and other pastoral communities,” he says. In particular, East Coast fever kills cattle kept by families trying to rise out of poverty. If researchers are successful, Nene notes, the entire region will have new reason to hope for a better life. Evans Taracha, ILRI project leader, also highlights the importance of strategic research partnerships to overcome this and similar diseases.

TIGR’s portion of the PNAS study was funded independently by TIGR and by sub-contract from the Animal Health Program of the United Kingdom Department for International Development, with previous contributions from J. Craig Venter and the ILRI for the T. parva genome project.

ILRI wins two top awards

ILRI vaccine developers won an award for Outstanding Scientific Article. Another ILRI team conducting research on savannah ecosystems shared an award for their innovative collaboration with Maasai landowners in Kenya.

Scientific Recognition

Each year, the Consultative Group on International Agricultural Research (CGIAR) recognizes the scientific contributions of the 15 agricultural research centres it supports through its Science Awards, presented at its Annual General Meeting (AGM), held each year in December.

At the CGIAR’s AGM held in Washington DC at the end of last year, scientists from ILRI and The Institute for Genomic Research (TIGR) picked up the award for ‘Outstanding Scientific Article’ for their paper, published in the top scientific journal Science, ‘Genome Sequence of Theileria parva: a Bovine Pathogen that Transforms Lymphocytes’. The team, led by Malcolm Gardner of TIGR, received a cash prize of US$10,000, which is being donated to fund travel for staff and students to attend conferences in this area.

The paper’s second author, ILRI scientist Richard Bishop, said: “We are delighted to receive this award. Our multi-partner collaboration and recent discoveries illustrate that African science is forging ahead – we are collaborating with world-class players and producing world-class science right here in Africa, for Africa.”

ILRI wins 2 awards

Pictured above from left to right: ILRI’s Director of Research, John McDermott, and TIGR scientist (and former ILRI staff member) Vish Nene, with the Award for ‘Outstanding Scientific Paper’. Looking on is ILRI’s Director General Carlos Seré and Bruce Scott, ILRI Director, Partnership and Communications.

Download TIGR/ILRI Press Release

Innovative Collaboration with Civil Society

The CGIAR also recognizes the contributions of innovative collaborations between CGIAR-supported centres and Civil Society Organizations (CSOs) through its ‘Innovation Marketplace Awards’. This year, 46 CSOs were invited to participate at the CGIAR Innovation Marketplace to showcase their collaborative work and share experiences.

ILRI’s collaboration with the Kitengela Ilparakuo Landowners Association (KILA) was one of four collaborations to win a Judges’ Award with a cash prize of US$30,000, to use for further collaborative work. ILRI has been collaborating with the Maasai of Kitengela Plains, located next to Nairobi National Park, in Kenya, since 2002. They have devised means to ensure that people, livestock and wildlife can live in harmony and have lobbied government to reduce fencing to allow the annual migration of wildlife though the Kitengela Plains, thus helping to prevent conflicts between wildlife and people and their livestock. Other collaborators of the program are Kenya Wildlife Service, Friends of Nairobi National Park, The Wildlife Foundation and Kajiado County Council.

The prize award was collected by ILRI’s CSO representative Ogeli Ole Makui and ILRI’s Mohammed Said. Makui said: “This award means so much to us. Our major challenge is to move forward and continue with the collaboration to help the community move forward. The Landowners Association will be using the prize money to fund further collaborative work.

ILRI wins 2 awards

Pictured above, from left to right: CGIAR Chair and Vice President of the World Bank Kathy Siena, the Program Officer of the Kitengela Land Lease Program, Ogeli Ole Makui and ILRI scientist Mohammed Said.

Download the award-winning poster

ILRI Awards

Dr Carlos Seré , ILRI’s Director General, said: “ILRI’s work is frequently recognized at the CGIAR’s annual awards. Each year the bar is raised and this year was no exception. Competition was tough with a very high standard of entries in all categories. We wish to extend our congratulations to the winners from our sister centres and are delighted that ILRI has won two of the top awards this year. This recognizes our commitment and contributions to both science and society.”

ILRI wins awards

Pictured above from left: ILRI Directors Carlos Seré and Bruce Scott and the President of the World Bank, Paul Wolfowitz at the CGIAR exhibit booth at the AGM in December 2006 in Washington, DC.

Research breakthrough against cattle killer

Innovation, capacity building and partnerships to combat a deadly African cattle disease are in the news. This month, ILRI's East Coast fever research is featured in two top journals – Science and the Journal of International Development. On 1 July 2005, America's leading scientific journal Science reported on the genome sequencing of a deadly parasite, Theileria parva, which causes East Coast fever (ECF), an infectious tick-borne disease that kills two cows every minute in Africa. This ground-breaking research was led by scientists at the International Livestock Research Institute (ILRI) in Nairobi Kenya, and The Institute for Genomic Research (TIGR), based in the USA. In addition to advancing research into parasitic livestock diseases, this research will also be valuable to scientists studying human malaria and cancers. TIGR/ILRI News Release ILRI News Backgrounder The ECF project is also of great interest to international development practitioners and policymakers. An article published in the July edition of the Journal of International Development by James Smith of Edinburgh University uses the ECF project as a case study example of how institutional research and development is changing. The old model 'technology-led' projects, often criticised for failing to deliver effective and affordable products downstream, is being replaced with  new model partnerships that have innovation and capacity building built in and that aim to deliver demand-led products of benefit to the poor in developing countries. Smith describes the ECF project as 'a potentially new model of… research and development partnership' which is an example of “a more ‘complete’ approach to innovation”. The ECF project has many partners and a very clear product focus. The project builds capacity in new ways, as those involved are forced to break out of their traditional boundaries. Scientists who were interviewed felt the project was encouraging them to think in new ways – like farmers and like businesspeople. There are many examples of 'good' technologies still sitting on shelves because scientists failed to consider the needs and circumstances of the end users of the technologies, such as whether the product would be accessible and affordable to farmers. International development professionals and donors are becoming increasingly focused on capacity building, partnerships, innovation systems and, ultimately, the delivery of tangible results, including products, as integral parts of R&D activity. There is a shift away from projects that could be described as 'research for the sake of research' to demand-led research, operated by many partners as a collaborating network that accomplishes a specific goal. John McDermott, ILRI’s Deputy Director General – Research said: 'The ECF Project illustrates ILRI’s new modus operandi, which generates innovation through strategic partnerships. Each partner is doing what they are best at – with the shared goal of delivering an effective and affordable vaccine for East Coast fever that will ultimately benefit millions of small-scale farmers in Africa.' There are lessons to be learned and the ECF project experience looks likely to be scrutinised further to gain more insights into new ways of doing R&D for greater benefits to the world's poor. Smith concludes: 'The East Coast fever vaccine project does appear to offer a new approach to prioritizing research and design, building capacity, and eventually producing an efficacious product. It does appear, however, that the positive spin-offs from the approach may not have been pre-planned but that the approach was shaped by a combination of the contingencies of vaccine production and the realities of institutional R&D in Kenya. The trick will be to identify exactly what makes this approach successful…'.