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Investigating the Molecular Mechanisms of Disease Goes Digital

Clemente Aguilar with friends, computational biology
Computational biologist Clemente Aguilar with two friends. (Image credit: NIMBios.)

This ScienceLives article was provided to Live Science in partnership with the National Science Foundation.

While studying veterinary medicine in Mexico, Clemente Aguilar most enjoyed the practice of surgery. But then methods to investigate molecular mechanisms behind disease via computation drew him into the field of computational immunology.

Now, as a postdoctoral fellow at the National Institute for Mathematical and Biological Synthesis, which is funded by the National Science Foundation, Aguilar uses genomic data and proteomic data (data related to proteins) to develop mathematical models designed to increase understanding of molecular structures and interaction — work that ultimately might aid the development of drugs and vaccines. Currently, he's investigating the structure of the Trypanosoma cruzi parasite, a particularly pernicious parasite that causes Chagas disease, which affects millions of people.

Name: Clemente Aguilar Age: 42 Institution: National Institute for Mathematical and Biological Synthesis Hometown: Saltillo, Coahuila, Mexico Field of Study: Computational Immunology

What is your field and why does it inspire you?

As far back as I can remember, I've been passionate about understanding nature, in particular living things. I chose to go into veterinary medicine because I like animals and I'm concerned about their health, but also because the well being of animals impacts the well being of humans.

As time passed, I became very interested in deeply understanding molecular mechanisms of disease. As a veterinary student, I worked in a laboratory dedicated to genomics and studied the genomics of the dog. It fascinated me that a computer program could trace the evolutionary process of genome reorganization based on DNA sequences. And it surprised me that mutations in an organism could be detected with a piece of software, and that the same software could tell us which mutations were related. Most startlingly, I learned that the molecular basis of disease could be modeled with computers.

Please describe your current research.

My research centers on using available genomic and proteomic information to develop computational methods that can expand our knowledge of molecular mechanisms of disease and increase the speed of development of immunotherapies and vaccines. The model organisms that I use for my research are parasites. One of them is Trypanosoma cruzi, the causative agent of Chagas disease, which affects millions of people in Latin America and is an emerging infectious disease in the United States.

What is the primary aim of your research? My goal is to develop efficient algorithms to predict molecular structures and molecular interactions that ultimately can assist in the development of drugs or vaccines.

How does your work benefit society?

Constructing new ideas to increase the knowledge about any area of research is the main benefit of science to society. In my case, building new methodologies to characterize molecules that have a direct impact on human health are my main contribution.

What do you like best about your work?

Three main things: first, the challenge of extracting new knowledge from data that is derived from biological experiments and is often publicly available; second, I like the people I interact with. As a computational biologist I am often part of a research team that involves mathematicians, computer scientists, chemists and biologists, and in learning to speak their "language," I learn from their fields. Finally, I enjoy mentoring students and helping them reach their goals.

What is the best professional advice you ever received?

When I was switching from veterinary medicine into computational biology I struggled to adapt to a whole new field, and needed a complete mindset adjustment. In particular, I struggled with advanced mathematical courses. In veterinary medicine, of course, you need a solid understanding of mathematics for personal and business finances, proper calculations of nutrient needs for animal nutrition, proper dosing of pharmaceuticals and proper administration of anesthesia. But you don't have to develop algorithms, program computers or apply statistical models to extract information from molecular data. To understand disease, I had to adapt to all these new strategies and tools, which was not an easy task. It was then when my wife reminded me that my goals were greater than the obstacles I was facing. I just needed to work harder and persevere.

What is the most surprising aspect of your work?

To me, it is still surprising that I can have my lab in my own personal computer, which contains many tools to analyze data that I can download from databases containing a wealth of information. I can also connect to powerful systems to run simulations. With all those tools, it is possible to arrive at accurate conclusions with mathematical models before performing biological experiments. Many aspects of biological systems can be better simulated quantitatively and hence their properties can be predicted. Often, such properties might not be evident to the experimenter until analysis reveals them.

What exciting developments lie in the future for your field?

Biologists are relying more and more on mathematical and computational techniques to do their jobs. Computational immunology has the potential to enable the identification of prospective allergens in genetically modified drugs and foods, understand the behavior and spread of infectious disease, understand the nature of specificity in immune network and immunogenicity, and predict growth and surface antigens on cancer cells, just to name a few examples.

Who is your #1 hero and why?

I don't suffer from idolatry, and so it's hard to place a single individual as #1. However, the characteristics that people I admire have in common are that they possess great intellectual fortitude, are capable of challenging ignorance and of remaining humble. I can name some of those whom I see as great individuals: Socrates, Jane Goodall, and José María Morelos (a Mexican Roman Catholic priest and revolutionary rebel leader who led the Mexican War of Independence movement).

What do you do when you're not in the lab or out in the field?

I like to keep in shape by practicing martial arts and going to the gym. Photography is one of my main hobbies, and in my free time, I like to read, mainly novels or books about science, history and philosophy.

Editor's Note: The researchers depicted in ScienceLives articles have been supported by the National Science Foundation, the federal agency charged with funding basic research and education across all fields of science and engineering. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation. See the ScienceLives archive.