Research Statement from PhD App (Oct2024)

During my undergraduate years, I focused on one main objective: to develop a strong theoretical foundation and powerful problem-solving abilities. The dream of becoming an impactful research scientist was well-fortified by my 3rd year, and the perspective behind this goal was strongly influenced by the ideas of Popper, Polya, and Feynman. Based on this, I actively searched for a mentor.

I joined Hinrich Boeger’s lab mainly because our scientific philosophies and temperaments were a good fit. The other reason was his resume: he did a 7-year Post-doc under Roger Kornberg during the period when his ground-breaking work in transcriptional regulation and chromatin biology was published. As my professor in advanced biochemistry, he taught me how to apply conceptual understanding and deductive reasoning to solve complex problems. For the first time in my scientific journey, mastery of this complex subject became a real possibility, and this greatly amplified my confidence and motivation. In his course on eukaryotic gene expression, our debates / explorations into the mysteries of transcriptional regulation and chromatin dynamics often continued late into the evening. My understanding deepened and viewpoint expanded with every interaction. Hinrich invited me to actualize my ambitions in his lab for my undergraduate thesis; and to keep the momentum going, he sponsored my master’s program.

My 20 months in the Boeger Lab centered around the regulatory relationship between nucleosome dynamics and chromatin structure and how dysregulation promotes genomic instability, or aneuploidy, in budding yeast. Specifically, I sought to better understand the mechanism of the histone chaperone Asf1, which uses a histone acetyl transferase (HAT) to modify a lysine residue on histone H3 (forming H3K56Ac) during S phase of replication. Since both hypo- and hyperacetylation strongly predispose the cell toward aneuploidy, my hypothesis is that the acetyl group on new nucleosomes suppresses the licensing factors that form the origin of replication complex (ORC). This should lead to two outcomes: under-acetylation, which would increase the odds of origin refiring during S phase; and hyper-acetylation, which would inhibit proper ORC assembly at the appropriate location prior to S phase. Both cases should promote, albeit by two different hypothetical mechanisms, inappropriate partial and whole chromosome duplications, a pattern associated with several cancers. To test these predictions, I first developed several mutant cell lines that mimic permanent states of hypo- and hyper- acetylation with fluorescent reporters driven by a constitutively active promoter. The relative intensities of the different fluorophores could then be used as an indicator of copy number variants of that locus using flow cytometry. Using time-course measurements of the different mutant populations, the number euploid cells with a 1:1 ratio of fluorophores, should diminish over time if missegregation was the primary cause of aneuploidy and should not be diminished if inappropriate re-replication was the dominant mechanism. The results showed full retention of the euploid population, which supports the hypothesis that improper acetylation of H3K56 promotes aneuploidy via re-replication, not missegregation. This was further corroborated by determining the mutation rate using a modernized version of the Delbruck-Luria fluctuation analysis method. I provided the above as an example my general reasoning process and approach to exploring interesting and relevant questions in the lab.

Throughout my first year in the master’s program, I continued to advance this line of research using different mutant / genetic approaches (knockouts, -ins, -downs, anchor-away systems), single-molecule chromatin accessibility and methylation sequencing (nanoNOMe), MNase digestion, and topological analysis (technique that uses DNA supercoiling and topoisomerases to quantify nucleosome number). Although my investigations were stimulating and rewarding, my scientific perspective gradually shifted. I realized that complex problems must be addressed in an interdisciplinary and collaborative manner and that effective research requires skillsets that support this approach. This insight led me to the lab of Tal Sharf. Tal’s research endeavor is, in my opinion, the most important one in human history—to map the brain’s neural circuits and understand how their interactions generate the emergent properties of function (sensory processing, cognition, behavior, states of consciousness, etc).

Unlike the human genome, which transmits information at a sub-cellular level, it is possible that the brain processes and transmits functional information through the activity patterns between assemblies of neurons. Primarily, the methods being developed in our lab are aimed at examining and manipulating the activity of every neuron with respect to every other neuron in a functional circuit. The research I am developing will employ a “back-engineering” strategy that aims to elucidate normal circuit function by examining pathological states.

I am interested in the early drivers of neurodegeneration, specifically, Parkinson’s disease (PD), which is characterized by degeneration of dopaminergic circuits in the midbrain. Despite aggressive, world-wide research initiatives, the causal mechanisms of PD have been difficult to parse for several reasons: for one, animal brains often fail to recapitulate key aspects of human circuit behavior and connectivity; another is that PD symptoms manifest after irreparable damage to the midbrain has already occurred; and finally, the triggers of the disease appear to be multifactorial, with myriad environmental and genetic influences, further convoluted by the multiple systemic pathways communicating with each other and the brain. I am currently working with Tal and others to refine a model that addresses these limitations and provides impactful, new insights that advance our fundamental knowledge of midbrain circuitry. In addition, my hope is that this research will lead to the development of diagnostics and therapeutic interventions targeted to the early triggers of PD and possibly other neurodegenerative disorders. For at least the next five years, my energies will be one-pointed on this objective, working together with some of the best and brightest individuals I have ever known.

Beyond my Ph.D., there are several appealing avenues. Perhaps it will make sense to do a Post-doc; alternatively, a role in industry may seem like the best option; or I may decide to start a company. What I do know is that my fundamental ambitions and motives will only deepen. For the good of humanity and for my own joy and fulfillment, I will be passionately engaged in solving a complex and important research problem with exceptional people. I will be striving to learn and develop myself as a human and as a scientist. I will be immersed in the thrill of the unknown, excitedly trying to catch a glimpse of the yet-to-be discovered.