Dr. Steve L. Bonilla

Dr. Steve L. Bonilla is a postdoctoral fellow currently working at University of Colorado, Denver with Prof. Jeffrey Kieft.  Notably, he is also a recipient of the prestigious HHMI Hanna H. Gray postdoctoral fellowship. He obtained his BS in chemical engineering from University of Washington and his PhD in chemical engineering from Stanford University. Dr. Bonilla’s PhD dissertation in the group of Prof. Herschlag focused on single-molecule and high-throughput studies of RNA 3D folding thermodynamics.

Dr. Bonilla uses cryo-EM to study RNA structural dynamics and is excited about “being able to see RNAs in multiple conformational states in a single experiment”. He was originally drawn to “the interesting and intricate viral RNA structures, which are the Kieft lab’s specialty, e.g.the exonuclease resistant RNAs in Dengue and Zika viruses”. He elaborated, “These structures prevent the viral genome from being fully degraded by the host, resulting in the formation of subgenomic fragments that are essential for the viral lifecycle. Structurally, xrRNAs are very interesting and I think still puzzling, because they are able to block the ‘chewing’ of the exonuclease Xrn1 by forming a ‘knot’ that topologically prevents the nuclease from progressing with its degradation. It was my interest in these structures, and other viral RNA structures, that motivated me to pursue a postdoc in the Kieft lab.” Regarding his attraction to Kieft lab, Dr. Bonilla further divulged that “I read Kieft lab’s papers very early in grad school, and I knew since then that I wanted to do my postdoc with Dr. Kieft. I could easily envision how my training in RNA structure thermodynamics and kinetics from Herschlag lab could transfer to the study of viral RNA structures and the processes they regulate.”

His recommendation to students is “to prioritize their mental health and to not hesitate to talk to someone (either a professional or a friend/family member they are comfortable with) if they are feeling like their stress is getting to levels that are substantially interfering with their life outside of work”. Dr. Bonilla added “this is especially important for groups of people that come from backgrounds where seeking help for your mental health is still stigmatized or not taken seriously.”

Dr. Bonilla grew up in Guatemala and moved to USA with his family at the age of 19. He remembers many difficulties in the beginning of his scientific career. “It was very challenging at first. I started my education in the US at the community college, taking night ESL (English as a second language) classes while working at a fast-food restaurant during the day. Little by little, I found my way into science and academia.” Graduate school was the biggest challenge in his career so far. “Grad school was tough. Work in the lab was challenging combined with classwork and problems outside of the lab with my personal life.” Dr. Bonilla overcame these challenges by “keeping at it and working hard”. His recommendation to students is “to prioritize their mental health and to not hesitate to talk to someone (either a professional or a friend/family member they are comfortable with) if they are feeling like their stress is getting to levels that are substantially interfering with their life outside of work”. Dr. Bonilla added “this is especially important for groups of people that come from backgrounds where seeking help for your mental health is still stigmatized or not taken seriously.”

Charles Darwin has been a motivating figure for Dr. Bonilla during the difficult times. “I’m inspired by how much his ideas shaped the way we understand everything about the living natural world.” Dr. Bonilla offers an important piece of advice to starting graduate students, “Avoid jumping into a lot of different projects, since completing things takes much longer than what you expect. If that happens, you may find yourself much later without a defined project. Instead, I suggest spending a lot of time finding a good question to pursue.”

Dr. Bonilla’s favorite RNA is “the exonuclease resistant RNA (xrRNA) structures that are found in the 3' UTR of certain type of positive strand RNA viruses. Another favorite molecule of mine is the tRNA-like structure (TLS) of brome mosaic virus (BMV); but here I may be biased because this is the molecule I've been working with and recently published. What is really interesting about this RNA structure is that it can participate in very diverse viral functions (replication, translation, and encapsidation of the viral genome). We think that this multifunctional structure may undergo conformational changes to interact with the diverse machineries required for the different functions.”

Dr. Bonilla’s favorite paper in RNA is “Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding".  “Although there are no ‘exciting new findings’ in this paper, it taught me how to think about RNA structure formation from a rigorous thermodynamic perspective; also how to interpret the effect of mutations (or other things that change stability, such as different ions) using the same thermodynamic framework. It was one of those papers that I read many times in grad school and I will probably encourage my future students (assuming that I am able to become a PI) to read and understand.”

You can reach out to Dr. Bonilla through his twitter account @Steve_Bonilla.