Of plants and parasites: an interview with Yong Woo

I am a computational biologist interested in understanding how information other than that encoded directly by DNA is still passed on through cell division (a process called epigenetic inheritance), and can provide blueprints for natural life. The technologies to study these types of molecular information have improved rapidly in the last twenty years. I am essentially a data scientist; my job is to analyze and gain biological insights from these large data sets.

Actually, my original research direction was totally different from the research being published in eLife now. I joined the pathogen genomics laboratory in KAUST with a view to studying how epigenetic inheritance helps parasites adapt to their hosts. A couple of months before my arrival, I was asked by the head of the pathogen genomics group if I was interested in a project studying the evolution of parasites, which was expected to last six months. The project lasted three years but luckily, turned out to be fun and important.

Apicomplexan parasites, which include those that cause malaria and toxoplasmosis, are the most diverse single-celled parasites known to us. People have been wondering how the intricate molecular machineries of these parasites first arose. Many of the key components of the parasites’ machineries appear to have already been present in the algae that subsequently became parasites; these components were re-purposed for parasitic processes (Woo et al, 2015).

This finding is exciting to different people for different reasons. Parasitologists, including those interested in finding cures for malaria or toxoplasmosis, can now look for genes that are common to the parasites and the algae, since these may provide possible drug targets. For me, the finding is interesting for a different reason. One of the key questions in genetics is to what extent genetic information can encode not only the structure but also the regulation of proteins. Do new cellular features arise by building completely new structures or by re-purposing of already existing structures? We have shown that the latter is just as important, if not more so, than the former.

I am currently putting together a research program to study the epigenetic basis for heat acclimation. We and many others have observed that Arabidopsis thaliana can survive gradual but not abrupt temperature increases. Once acclimated, the plant survives better when later faced with heat stress. This sounds intuitive but how this is accomplished at the molecular level is not well understood. I am interested in understanding whether this memory is due to epigenetic information, i.e. what can be inherited through cell division that is not encoded directly by DNA. I am currently working with a PhD student on this question and I foresee that at least one more graduate student will be joining our group to work with us on this topic.

When I received the acceptance e-mail from eLife: I felt relieved and that three years of my effort were finally vindicated. Also, there were many moments of joy when we received valuable help from other contributors (i.e. other than me and the senior author) of the project. In particular, the second author of the paper, Hifzur Ansari, has spent countless hours collecting and curating gene sets or running basic pipelines, which were necessary for my analyses and synthesis of the findings.

This was a cross-disciplinary project conducted at multiple institutions on four different continents. Managing and coordinating the expectations of many people was not easy. Also, I was writing the manuscript full-time for a year, pretty much putting the plant epigenetics project on hold. Since I was trying to become an independent researcher in a field different from the project, I felt that I was regressing in my career even though the project was progressing.

I did three years of post-doctoral training with Professor Wen-Hsiung Li. Besides being one of the most accomplished scientists in the field of molecular evolution, he deeply cared for my scientific career. I try to emulate him when I work with a student: I try my best to care for him or her. The clarity of Wen-Hsiung’s thinking and how he focuses on the work in hand allows him to be extremely efficient. Honestly, this is where I need to learn more from him.

There has to be a way for scientists to work without unnecessary pressures. True, meaningful progress in science comes from people who care about science rather than by those who care about success in their careers. I think, right now, scientists are forced to think too much about surviving in their career instead of focusing on scientific questions. Some pressures are beneficial, but right now there is too much unnecessary pressure on scientists.

I am not sure… I am not being a pessimist but there are too many scientists and not enough positions. Perhaps I should leave the field, and try to reduce the supply side? LOL. On a serious note, there has to be an institutional effort to help early career scientists become independent.

Scientists face unique advantages and challenges here. There are many advantages, including the availability of ample funding sources under the right circumstances. For example, professors at KAUST have generous base-line research budgets, and they can also apply for research funding provided by the university.

I am learning how to speak Arabic.

Yes, my children are growing up, and it is difficult to turn off my research brain when I come home. Fortunately, my wife has decided to stay home to take care of the children, for which I am extremely grateful.

While I am still young (<40 years), I am beginning to understand that I won’t live forever. I would like to become an effective nurturer of the next-generation scientists to some capacity and to teach undergraduate students at some point.

I went from pharmacy (i.e. clinician) to pharmaceutics (i.e. applied science) to cancer genetics (i.e. “basic biomedical science”) to evolutionary genetics (i.e. “basic science”). I was afraid to try basic science because of poor job prospects but in the end, I found out that basic science is in my blood.

• 2012–present: Research Scientist, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
• 2009–2012: Postdoctoral Scholar, Wen-Hsiung Li Laboratory, University of Chicago, Chicago, IL, USA
• 2004–2009: Ph.D. in Functional Genomics, University of Maine, Orono, ME, USA
• 1998–2001: M.S. Pharmaceutics & M.A. Applied Statistics, University of Michigan, Ann Arbor, MI, USA
• 1994–1998: B.S. Pharmacy, University of the Sciences in Philadelphia, Philadelphia, PA, USA