Bioinformatics in Argentina to fight neglected diseases
Fernán Agüero was immensely excited when he entered the field of bioinformatics. With a background in molecular biology and parasitology, he helped local groups to sequence small fragments of DNA to discover new parasite genes. So exciting was the work, it led to a lifelong commitment to bioinformatics.
DNA analysis applied to parasitology was routinely used at home in Argentina, but not at the scale required to tackle complete genomes. Agüero had already specialised in parasite biology, even applying to study Trypanosoma cruzi (T. cruzi), the Chagas causing parasite, as an undergraduate biology student in Buenos Aires in the late nineties. His superiors soon realized he was primarily interested in bioinformatics but there were almost no research groups in this field in Argentina at the time.
"It's very easy to get into contact with parasitology in Argentina," he explains. "But bioinformatics was just starting to be mentioned. I was always working with computers so bioinformatics was kind of natural. I really liked it." A bioinformatics course at the University of Uppsala in Sweden enabled Agüero to combine two passions; dabbling in computers and parasite biogenetics.
TDR targets parasite genomes
When TDR issued a call for proposals for an international project incorporating genetic information of pathogens seen primarily in the developing world, Agüero wanted to get involved. As the human genome project progressed, researchers had begun to sequence the DNA of parasites, many funded by TDR. And, to make the most of this rich new resource, TDR decided to combine all sorts of vital pathogen information into a single database called TDRtargets.org, providing genomic data on pathogens, their expression and protein structures, chemical properties and drug information gleaned from published papers.
“TDR funding came at a time in my career when I was trying to establish a bioinformatics unit in the institute and to start recruiting students. And when you are young it is difficult to get funding.”
The idea was to help stimulate drug development for neglected diseases, says Professor Wesley C. Van Voorhis of the Centre for Emerging and Re-emerging Infectious Diseases (CERID) at the University of Washington and one of the team of experts gathered from all over the world to create the database. Agüero was charged with designing TDRtargets.org so users can easily interrogate it via the internet.
“Agüero is a leader and innovator in the field of bioinformatics in supporting target-based drug development,” says Van Voorhis. "He has written the code that runs the site, trained students and postdocs to run and curate the website, effectively reached out to users in the developing world, run workshops, and proven the usefulness of curating drug target information from the genomes of infectious diseases predominately found in the developing world. Without him, the site simply wouldn’t work at all!"
The experience was invaluable for Agüero. "It meant a lot to me because it was like five years with constant exposure to five mentors, not just one," he says. The database is still housed at his university in San Martín, on the outskirts of Buenos Aires where research groups from all over the world have accessed it. Agüero has used the database to pinpoint interesting targets within T. cruzi, and is testing them in mice.
Spreading the word on bioinformatics
Today Agüero, Assistant Professor of Bioinformatics and Computational Biology at the Instituto de Investigaciones Biotecnológicas at Universidad de San Martín, has helped create a sizeable community of bioinformatics experts in Argentina. He teaches bioinformatics to around 30 doctoral and postdoctoral students every year, based on a course he created in 2003.
Expertise in teaching came through TDR, which held an intensive month-long, train-the-trainers’ course in Rio de Janeiro, Brazil back in 2001. "That course was very important to foster development of expertise in the region. When we got back to our countries we could start to establish bio-informatics courses," says Agüero, who helped found Argentina’s only society for computational biology and bioinformatics (A2B2C).
“I think that supporting young researchers like Agüero has an amplifying effect and has undoubtedly paid off in terms of research capacity in developing countries, as well as in obtaining tools for disease control.”
Dr Alberto Carlos Frasch, Dean, Universidad de San Martín
He views the TDR funding as crucial in furthering bioinformatics in Argentina. "It came at a time in my career when I was trying to establish bioinformatics in the institute and to start getting students. And when you are young it is difficult to get funding," he says.
Dr Alberto Carlos Frasch, a senior member of Argentina's National Research Council and dean at Universidad de San Martín, agrees. “Here is an excellent example of the importance of international organizations like TDR supporting young researchers to allow their development into mature scientists in the area of neglected diseases,” he says. “I think that supporting young researchers like Agüero has an amplifying effect and has undoubtedly paid off in terms of research capacity in developing countries, as well as in obtaining tools for disease control.”
Today Agüero is hoping bioinformatics can improve one particular tool – diagnostic tests – by analysing bio-markers that might be more reliable than those detected in traditional tests. Today’s Chagas tests cannot tell if a drug has actually worked, for instance. Among the group of so-called neglected diseases, the need for bioinformatics is stronger than ever, since current screening technologies for new diagnostic markers generate large datasets. New biomarkers can be useful not only for individual diagnoses, but also for monitoring clinical trials, assessing the disease prevalence and emerging outbreaks.
For more information, please contact
TDR Communications Manager
Telephone: +41 79 441 2289