![[Feedback]](/icons/banner/feedbackACT.gif){kind=icon}
![[For Subscribers]](/icons/banner/subscriberACT.gif){kind=icon}
![[Archive]](/icons/banner/archiveACT.gif){kind=icon}
![[Search]](/icons/banner/searchACT.gif){kind=icon}
![[Contents]](/icons/banner/tocACT.gif){kind=icon}
|
|
|
|
|
||
|
Vol. 11, Issue 3, 319-322, March 2001
COMMENTARY
|
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 |
ARTICLE |
|---|
 TOP
 ARTICLE
 REFERENCES
|
|---|
When an undergraduate student in science from
Latin America is asked about career goals, the answer will probably
invoke dreams of using cutting-edge technologies to investigate the
frontiers of science. For these students, the realities of life in
their countries almost always reduce their options for achieving this goal to only one: Emigrate to a developed country. Although many of
these countries produce numerous international scientific papers relative to their small research budget (Macilwain 1999a
), their access
to the latest-generation technology is fairly limited. This is
particularly true in the field of genomics, in which the need for
automated, high-throughput equipment raises the cost even more.
However, when done wisely, genomics research and development has proven
to be an affordable reality for developing countries. Choosing the
right model organism, organizing laboratory networks instead of
megalaboratories, and concentrating funding on one large project
instead of splitting it among many smaller ones are the methods by
which genomics is succeeding in Latin America. The need for training
scientists in disease-endemic countries led the World Health
Organization (WHO) to pledge almost US $1 million to launch the Special
Program for Research and Training in Tropical Diseases (TDR), which was
the first broad genomic initiative involving Latin American countries.
The goal of TDR was to analyze the genomes of three protozoan and two
helminth parasites that seriously affect developing countries:
Trypanosoma cruzi (Chagas disease), Trypanosmoa
brucei (African sleeping sickness), Leishmania major
(leishmaniasis), Burgia malayi (filariasis), and
Schistosoma mansoni (Schistosomiasis). The TDR projects were meant to increase knowledge of the molecular biology of these parasites
and were especially oriented toward the development of therapies,
vaccines, and diagnostics. North-South and South-South collaboration
networks were organized so that expertise and technology could be
transferred and distributed throughout these networks (Degrave et al.
1997; Johnston et al. 1999). South American countries participate in
three of the five networks (T. cruzi
[http://www.dbbm.fiocruz.br/TcruziDB/index.html], leishmania
[http://www.ebi.ac.uk/parasites/leish.html], and schistosoma [http://www.nhm.ac.uk/hosted_sites/schisto/index.html]), together with many developed and developing countries around the world. Moreover, the T. cruzi network was coordinated by a South
American investigator from the Institute of Technological
Investigations at the National University of General San Martín
(IIB-UNSAM), Argentina (Trypanosoma cruzi Consortium 1997),
and a modest Schistosoma EST sequencing project had begun
earlier in Brazil (Pena 1996). After five years, most of the specific
aims of these collaborative efforts were achieved. Now a number of
resources are available for each parasite, including large insert
libraries, EST and GSS sequence data, physical maps, and databases.
These resources are distributed among the network participants and the
community through the Web. WHO's funding for these initiatives was
fairly limited and was intended to be the primer for obtaining
additional funding from other agencies. Indeed, parasite full-genome
sequencing projects are now supported as a consequence of these early
efforts. A remarkable case is that of T. cruzi, a protozoan
causing the Chagas disease, which chronically or fatally affects
millions of people in South America. This parasite received little
attention from funding agencies before the WHO decided to fund the
genomics project. The investment proved to be successful, as sequencing
and mapping data became available from the collaborative network
(Ferrari et al. 1997; Verdún et al. 1998; Santos et al. 1999;
Agüero et al. 2000; Porcel et al. 2000) and the goal of
attracting more funding agencies to extend this research was achieved.
Recently the National Institute of Allergy and Infectious Diseases
(NIAID) from the National Institutes of Health (NIH) assigned a grant to the Institute of Genome Research (TIGR), the Seattle Biomedical Research Institute, and the University of Uppsala to sequence the
T. cruzi genome. This outcome is fortunate for the T. cruzi research community because the availability of extensive
genomic data will accelerate the development of therapeutic and
diagnostic tools. Nevertheless, it highlights the usual governmental
policy in developing countries: not to fund basic research unless an applicable product can be obtained in the short term. When basic research is in the area of genomics, it is even harder to convince the
local funding agencies to devote a substantial fraction of the research
and development budget to a single, but very large, basic project that
would yield just the raw materials for the preferred applied research.
Preferential support for applied research seems to be the trend in the
scientific funding policies of developing countries. This makes sense,
considering the large international public efforts to generate and
release genomic data to the public. Why would it be worth devoting the
small resources available in developing countries to joining in this
effort when there are so many other health and environmental problems
in the Third World to be taken care of? This "applied versus basic"
argument has long been present and was raised again a few years after
the beginning of the T. cruzi genome project (Trypanosoma
cruzi Consortium 1997). Paradigmatically, in spite of their
efforts, groups conforming the T. cruzi network could not
obtain local funding to complete the genome sequence. As a consequence,
the job ended up being done by labs in developed countries. For the
supporters of the "applied" policy, proof of the wisdom of their
argument was that even without cutting-edge technology and the full
T. cruzi genomic sequence data, several South American
countries have been recently declared free of Chagas disease
(http://www.who.int/tdr/diseases/chagas/default.htm).
However, biological diversity is too large to assume that all the
valuable genetic information is already in public or private databases,
and the value of genomics is not just in sequence information. It is
also in the development of technology to generate and analyze genomic
data, which in turn could lead to useful products. This was clearly
seen by Brazilian scientists and policymakers from the state of
São Paulo. In 1997, the state science funding agency of São
Paulo (FAPESP) committed more than US $11 million to completely and
accurately sequence the genome of Xylella fastidiosa, a
phytopathogen that threatens orange cultivation, a major industry
within this region (Bonalumé 1997). The funding received by this
project alone represented a substantial proportion of the entire
Brazilian research budget. Nevertheless, this bacterium was deemed
agriculturally and economically important enough to be worth the
effort, although knowledge of its complete genetic information would
not give any short-term applied benefit to citrus producers. Despite
this, the São Paulo state citrus growers' association
(Fundecitrus) also contributed US $500,000 to the project (Macilwain
1999b), demonstrating their confidence that this basic research would eventually yield practical benefits for citrus production.
The significant amount of genomic information expected to come from the
X. fastidiosa genome project has not been its only benefit.
Thirty labs in the São Paulo region have been equipped and
trained in state-of-the-art technology instead of creating a center
dedicated to the project. These laboratories were organized as a
network known as the virtual institute ONSA
(http://watson.fapesp.br/genoma3.htm). The strategy proved very
successful in getting the job done at a high standard of quality within
the planned 2-yr timeframe, as well as achieving the physical map
(Frohme et al. 2000; Xylella fastidiosa Consortium 2000). The
success was far-reaching: As an immediate consequence, FAPESP raised
its bet and increased funding for genomic projects. Now, three more
bacterial phytopathogens are being sequenced in São Paulo (a
grape strain of Xylella fastidiosa; Leifsonia xyli ssp.
xyli, a sugarcane pathogen; and Xanthomonas citri,
another citrus pathogen), and a call has been issued for proposals to
sequence several more. Complex genomes, such as that of sugar cane, are
also being analyzed by EST approaches in which other Brazilian states
are participating. Expansion of genomics efforts outside São
Paulo is being promoted by the federal government through the creation
of more ONSA-like networks (Macilwain and Bonalume Neto 2000). The
São Paulo initiative also gives an example of the technological
development often derived from ongoing genomic projects. After being
preliminarily assayed in the S. mansoni genome project in
Brazil (Dias Neto et al. 1997), the ORESTES technique (open reading
frame ESTs) became an optional approach for obtaining human EST
sequences spanning the open reading frames (de Souza et al. 2000; Dias
Neto et al. 2000).
Thus, the effort invested by Brazil is paying off. Having shown that
Brazilian labs are up to date with genomic technology, the Federal
University of Pelotas became a member of the International Rice Genome
Sequencing Project (IRGSP; Eckardt 2000). But perhaps the most
remarkable consequence of the Brazilian experience is the fact that
funding for genomic projects in Brazil is now also coming from abroad.
The United States Department of Agriculture (USDA) is financing
one-half of the US $500,000 that the sequencing of the grape strain of
X. fastidiosa will cost, and the United States-based
Ludwig Institute for Cancer Research is supplying one-half of the US
$10 million that ONSA will use to produce up to one million ESTs from
human tumors.
All of these achievements have been celebrated in a range of media,
from the covers of scientific journals to the New York Times,
as well as in local newspapers and on television. In some cases, this
might have offered a false image of abundance and prosperity in
Brazilian science, which could compete with leading labs worldwide to
attract young Latin American scientists. Several Brazilian scientists
working either in Brazil or the United States disagree with this image
of generalized scientific prosperity in their country (Hötzel
2000; Prolla 2000). But the unquestionable merit of the Brazilian
endeavor is yielding invaluable fruits and will hopefully catalyze
improvements in the country's scientific system.
Following the same track as Brazil, Mexico has also engaged in bacterial genomics. Two megaplasmids from the nitrogen-fixing bacterium Rhizobium etli have been sequenced, and the complete genome sequence is in the pipeline in the Center for Research in Nitrogen Fixation (CIFN; http://itzamna.cifn.unam.mx) at the National Autonomous University of Mexico (UNAM). Funding for these projects comes from the National Council for Research and Technology (CONACYT), which has also recently made a significant gamble in assigning a US $2 million grant to the Center for Advanced Research Studies (CINVESTAV) to carry on a maize functional genomics project. This investment represents 2% of the country's current yearly research and development budget, comparable to the proportion of the United States National Science Foundation (NSF) budget assigned to new plant genomics projects in recent years. One goal of the maize functional genomics effort is to gather sequence information for agriculturally important maize genes. In this way, they can seek legal protection for genes particularly relevant to local production. Another goal is to train human resources in new technologies, now absent in the country, that in turn will allow the Mexican scientific community to participate in future postgenomic international projects.
Other countries, such as Argentina, are still discussing whether they
should make real investments in genomics. Meanwhile, some researchers
in these countries are trying to keep up with genomic technology by
maintaining their participation in the international networks or by
generating new lower-scale projects, such as the genomic analysis of
the sunflower, which is being carried out by several groups at the
National Institute of Agricultural Technology (INTA). These researchers
have begun sequencing several thousand sunflower ESTs as well as
constructing a BAC library and mapping the genome using several
approaches (N. Paniego, M. Echaide, M. Muñoz, L. Fernández, S. Torales, P. Faccio, I. Fuksan, M. Carrera, R. Zandomeni, E.Y. Suárez,
and H.E. Hopp pers. comm.). Other research groups at the same institute
in collaboration with the IIB-UNSAM carried out a medium-scale genomic
sequencing project aiming at gene discovery in the cattle pathogen
Brucella abortus (Sánchez et al. 2001). The IIB-UNSAM is
now using internal money to pursue the genomic sequencing of
Campylobacter fetus, another cattle pathogen.
Interestingly enough, the Max Planck Institute in Goettingen, Germany, has decided to support the creation of a center for genomics at the National University of La Plata. This initiative was launched together with the Association of Universities of the Montevideo Group (AUGM), which includes several South American countries. The joint initiative will represent an investment of several million dollars. By the end of 2001, when the center is expected to open, several research groups will be established and ~25 people will be hired. Perhaps this will mark a change in Argentinean politics regarding investing in genomics.
There are certainly many young Latin American scientists willing to take open positions to work on genomics. This was evident by the 110 applications to participate in a recent practical course on genomic sequencing and annotation (http://www.hhmi.org/grants/international/educate/past.htm; http://genoma.dna.uba.ar:8080) held at the Institute for Research in Genetic Engineering and Molecular Biology (INGEBI), Buenos Aires, and organized by the US National Academies with funding from the Howard Hughes Medical Institute (HHMI) and the Argentinean-Brazilian Center for Biotechnology (CABBIO). Nineteen students from eight Latin American countries had a chance to experience high-throughput genomics and, perhaps more important, to interact with experts from leading institutions and companies like the Genome Sequencing Center at Washington University, Cold Spring Harbor Laboratory, the Microarray Database at the School of Medicine from Stanford University, the Ludwig Institute for Cancer Research, (São Paulo, Brazil) and Cereon Genomics (Cambridge, MA). Among the students, there were members of some Latin American laboratories that are beginning to get involved in genomic sequencing projects. Genomics-related events such as this course, which are thus far fairly unusual, constitute a way to train people and establish collaborations between Latin American laboratories and strong genomics institutions in neighbor or central countries.
Clearly, the importance of being part of the new era in biology is becoming more and more evident in Latin America. Successful examples have proven that it is possible to do genomics and that these efforts generate resources and expertise, promote technology transfer, allow participation in international initiatives, and attract funding. By no means will they immediately create a scientific paradise, but these early efforts are definitely helping Latin American countries to increase their scientific impact at the international level and to stop their brain drain. The generalization of these ideas might very well be the way for these countries to recover their scientific future: those rising students who emigrated in search of scientific frontiers.
| |
ACKNOWLEDGMENTS |
|---|
I thank Anamaria Camargo, Alberto Carlos Frashc, Mariano Levin, Jean Phillipe Vielle, Rolando Rivera-Pomar, Victor González, Esteban Hopp, and Michael Ronemus for supplying information and critical reading of the manuscript.
| |
FOOTNOTES |
|---|
1 Corresponding author.
E-MAIL rabinowi{at}cshl.org; FAX (516)367-8369.
Article and publication are at www.genome.org/cgi/doi/10.1101/gr.179501.
| |
REFERENCES |
|---|
|
TOP
ARTICLE
REFERENCES
|
|---|
CiteULike 
Connotea 
Del.icio.us 
Digg 
Reddit 
Technorati What's this?
This article has been cited by other articles:
|
|
 |
|
  T. D. N. Silva, L. C. da Cunha Aguiar, J. Leta, D. O. Santos, F. S. Cardoso, L. M. Cabral, C. R. Rodrigues, and H. C. Castro Role of the Undergraduate Student Research Assistant in the New Millennium CBE Life Sci Educ, December 1, 2004; 3(4): 235 - 240. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
