In search of partnerships and applicability of results

For researcher Daniel Janies of UNC Charlotte, one of the organizers of FAPESP Week North Carolina, now is a good time to expand scientific cooperation with Brazil

By Samuel Antenor, in Raleigh

Agência FAPESP – Since first taking part in FAPESP Week in Washington, DC in 2011, Professor Daniel Janies of the Department of Bioinformatics and Genomics at the University of North Carolina at Charlotte (UNCC) has sought to strengthen research partnerships between universities in Brazil and the United States.

Janies was one of the organizers of FAPESP Week North Carolina, held November 11-13, 2013, which brought Brazilian and U.S. researchers together at the University of North Carolina at Charlotte, the University of North Carolina at Chapel Hill, and North Carolina State University in Raleigh.

With extensive experience in genomics and bioinformatics, Janies taught at Ohio State University’s College of Medicine at the School of Biomedical Sciences between 2003 and 2012, and he is currently a professor at UNCC, where he moved in August 2012. He is also a researcher in the Assembling the Tree of Life (AToL) program sponsored by the National Science Foundation (NSF), which brings together researchers from various countries and different fields to reconstruct the evolutionary connections of all living things.

In an interview with Agência FAPESP during FAPESP Week North Carolina, Janies talked about the importance of joint research in various countries, of the efforts to bring together researchers from universities in the U.S. and Brazil, and about the results achieved through partnerships and joint strategies between institutions from both countries.

He also commented on advances in bioinformatics, whose studies can be related to problems in various areas in order to obtain common results to seemingly distinct questions, such as the evolution of species, the discovery and conservation of biodiversity, and protection of human health.

Agência FAPESP What is your opinion, in general, about the agreements signed between universities from various countries and their results in terms of joint proposals and study visibility?

Daniel Janies – Scientific problems are universal and interest in solving them exists at various universities in different countries. People think in a variety of ways. The cultural differences are fascinating, and if you can draw on complementary strengths, these collaboratons lead to positive results. Today, scientsits are able to work together and exchange ideas more quickly, whether in person or by using the Internet. Research cooperation is very common in our fields – genomics and bioinformatics. That’s how it was when I was at Ohio State University and that’s how it is here at UNC Charlotte, where partnership will be started and strengthened as a result of FAPESP Week.

Agência FAPESPWhat results have been achieved since you first participated in this type of conference in 2011?

Janies – After the first FAPESP Week in the U.S., in Washington, DC, Ohio State University, which already has offices in Shanghai [China] and Mumbai [India], turned to Brazil and may ultimately open an office São Paulo. Specifically with FAPESP Ohio State entered an agreement worth 1.4 M USD and has thus far funded 24 joint awards. As the relationship between the United States and Brazil contains so much potential there needs to be more U.S. federal support for our joint efforts. We have a good start. For example the U.S. government supported our initiative by providing NSF funding to bring U.S. based researchers to the 2011 edition of FAPESP Week in Washington, DC. Similarly, we’ve been able to obtain funding from a variety of sources, U.S. and international, to participate in and organize symposia and short courses in Brazil. This week I was happy to hear that FAPESP has entered agreements with the DOE and NIH.

Agência FAPESPDo you think, then, the relationship between U.S. researchers an FAPESP is significant?

Janies – It certainly is. We have an excellent relationship with FAPESP, which I got to know as a researcher while doing my postdoc at the American Museum of Natural History in New York when I had colleagues who were Brazilian fellows from the Foundation, although I didn’t know exactly how FAPESP worked. Since then, the relationship has gotten better, culminating in the 2012 signing of a memorandum to initiate a joint call for proposals in 2013 between FAPESP and the Ohio State University, where I worked as an associate professor.
We are working hard to illustrate how mutually beneficial the relationship can be. For example working with Brazil provides tremendous opportunities in biodiversity and natural products chemistry. Cooperation is also important in areas of research such as neglected tropical diseases and global diseases because pathogens can quickly move throughout the world. In infectious disease research, we have research partnerships in Asia, Africa and Europe. I also work with researchers across Brazil, for example in Rio de Janeiro and Recife. It is now a very good time to begin new research partnerships with Brazil.

Agência FAPESPDo administrators in the institutions view this relationship more as a curiosity or are they purposely acting to build specific partnerships?

Janies – There is a spectrum of interest. For some the relationship is a curiosity, while others are acting purposely. Part of my mission in North Carolina is to continue open the doors to joint research with São Paulo-based scientists. Some administrators are working with us, but others need further clarification. Fortunately the U.S. federal government recognizes the importance of partnerships with Brazil in areas such as chemistry and biodiversity. Joint FAPESP-U.S. research projects are being funded by the NSF in the United States, because the topic is important and joint work improves our diplomatic relationship.

Agência FAPESPHow is the mood for support to joint research with foreign universities at this time, in the U.S., especially in countries that today represent a new frontier in scientific research, like China, India and Brazil?

Janies – The federal government is willing to support joint research because it knows that this is important. Some U.S. states know it as well, but there are others where work needs to be done to explain why international research agreements are needed because not all of them share the federal government’s position with regard to this. There have historically been partnerships with Japan and several European countries. There are also partnerships with China and India, and only recently with Brazil, although the relationship with Brazil is extremely important for us. I also foresee improved relationships based on scientific cooperation with countries in Africa, especially South Africa.

Agência FAPESP Are there specific cases that could lead to partnerships with Brazilian universities in bioinformatics or other fields more directly related to industry?

Janies – In my view, and with specific regard to São Paulo, we have had numerous independent conversations about joint research in bioinformatics. Something that we’re doing here, for example, is to study the use of lower cost platforms for genomic sequencing, which means applying the technologies to diagnostics and work in the field of biodiversity. However, low cost sequencing is only part of the solution. It’s relatively easy to obtain raw data on a sequencing platform, but the bigger challenge is to have people trained to be able to analyze data and produce actionable results. That’s exactly what we do here in the Department of Bioinformatics at UNCC. We train people to work on important problems that can be addressed with genomics and bioinformatics. Substantial investments in bioinformatics are being made in São Paulo like with the Lactad [the Central Laboratory for High-Performance Technologies at the University of Campinas], and I think it’s important for us to have a partnership in this area because we have excellent curricula here and could have student exchanges and doctoral programs specifically designed for this area. We can also exchange professors between laboratories in São Paulo and Charlotte. As long as we have funding opportunites from each side, and a mutual understanding of expectations, the sharing of equipment, knowledge and people is a good strategy for investing in research.

Agência FAPESPDoes this type of agreement also interest companies that would like to develop technologies related to these research partnerships?

Janies – Absolutely. Bioinformatics is a very interesting field because, for example, when the first human genomes were sequenced between the late 1990s and the early 2000s, the expectation was that research would change very quickly. We used to think that it would be possible to conduct experiments to discover and confirm everything we needed for developing therapies just by using computers. However, today we know that the best research is done when empirical work is designed in close association with computing. With this strategy, bioinformatics is the glue that holds together the experimentalists and analysts in a research team. In other words, bioinformatics is not an Internet bubble – it is something that’s become pervasive across the sciences. Many scientists use bioinformatics in their research, for example in fields such as personalized medicine, agriculture, bioenergy, the natural sciences, infectious diseases and so on. There are examples of the growing use of genomic information to improve the quality of work done in all biomedical fields.

Agência FAPESPWhat expectations do you have regarding the use of bioinformatics over the next few years, including possible partnerships with researchers in Brazil?

Janies – Bioinformatics is already being used, and should be used even more, in biodiversity studies, leading to a better understanding of environmental issues. Two specific examples are joint research in biodiversity of the Atlantic Forest, in São Paulo, and of the genomics of sugarcane. In the sugarcane example, genomics and bioinformatics can be used to improve the production of ethanol. The choice of sugarcane in Brazil is science based – unlike the ethanol produced from corn in the United States for reasons more political than scientific. The entire process of genomic sequencing of plants is extremely difficult, but we can advance even more quickly with joint research. We are looking for possible intersections between studies conducted at our universities and those conducted in São Paulo. Bioinformatics and genomics are great starting points because these fields touch on many other important areas.

Agência FAPESPIn the research you presented during FAPESP Week North Carolina you mentioned the evolutionary the tree of life. From the multidisciplinary standpoint, what specifically would its dimensions and applications be?

Janies – It essentially involves finding similarities and differences in the anatomy and genetics of groups of organisms and using this information to discover their relationships on this phylogenetic tree. Animals can be organized into nested groups whether they be mammals, fish, birds or invertebrates. When these groups and other life forms such as plants and microorganisms are all connected via anatomical and genomic data this constitutes the tree of life.
Many researchers at universities in the U.S., Brazil and elsewhere share the use of phylogenetics. Phylogenetics is a central organizing structure for organismal groups joined by genomic and anatomical data. Therefore, phylogenies can also be called trees of life, which are branching diagrams, representing a hypothesis for relationship of organisms and changes that occur along the branches. Changes include mutations and alterations in anatomy and behavior. Although phylogenetics was conceived for taxonomy, this technique has been recently and widely applied in biomedicine.

Agência FAPESPWhy is this type of research important for use in biology and health?

Janies – Phylogenetic analysis became essential to biomedicine because, for example, the approach tells us which microorganisms are more closely related and therefore share important characteristics. Thus, the information obtained through limited experimentation about one strain may be useful in predicting the properties of another strain. This transitive property of phylogenetic inference helps biomedical scientists predict which strains are pathogenic or susceptible to drugs. The nature of phylogenetic analysis makes it valuable for human health because it allows us to make decisions about where and how to allocate resources for the prevention of emerging diseases. Projects like I describe here, that combine empirical and analytical research, with education in bioinformatics and genomics are what we emphasize at UNCC.