In a Tortoiseshell
This piece is an excerpt from my senior thesis midyear report. My thesis project draws on ideas in engineering, biology, and mathematics to model the growth dynamics of a genetically engineered yeast population. In this section, I describe the biological background of my project.
Excerpt
1.1 The promise of synthetic biology and metabolically engineered cells
Synthetic biology is the practice of applying engineering principles to biological systems, typically cells, redesigning them for targeted use. Synthetic biology draws parallels between cells and electronic devices, particularly by treating cells as controllable input/output systems enabled by four broad cellular subsystems: sensing, signaling, regulation, and metabolism (Del Vecchio and Murray 2015). Synthetic biologists manipulate these subsystems by changing or adding to a cell’s genetic material in order to make cells behave in defined ways. This process of “cutting and pasting” natural and synthetic pieces of DNA together and inserting them into a cell, called cloning, has been enabled by recombinant DNA technology, PCR (DNA amplification), and the ability to artificially synthesize DNA.
Synthetic biology ties closely to metabolic engineering, which introduces or optimizes cellular processes, typically to produce substances of interest such as pharmaceuticals, biofuels, and specialized chemicals (Markina, Kotlobay, and Tsarkova 2020). A key concern for metabolic engineers is how to scale engineered cells for industrial use: as therapeutic agents, for biomanufacturing of food and drugs, and for environmental efforts like water purification or carbon capture.
1.1.1 Complicating features of the cellular environment (Del Vecchio and Murray 2015)
Despite the seemingly ‘programmable’ nature of cells, unique challenges arise in the biological environment, making it difficult to achieve reliable behavior from engineered cells, and therefore to scale engineered populations to the extent required for industrial use.
Stochasticity: Even under controlled conditions, the behavior of a cell can be unpredictable, making experiments difficult to reproduce. Stochasticity is present throughout biological systems and may arise from external perturbations to the cell or internal processes like molecular binding and unbinding.
Mutation: When cells divide, they replicate their DNA. This is an opportunity for mutations, or changes to their DNA, to occur. Every so often, a cell may receive an “escape mutant”– a version of the DNA that nullifies the function of the engineered construct (Radde et al., 2024).
Competition for limited cellular resources: Exogenous (engineered) and endogenous (pre-existing) DNA compete for the same limited set of resources within a cell for reading and executing the instructions they contain. Thus, introducing new DNA into a cell detracts from its ability to perform essential functions like growth and division. This metabolic burden, or stress, causes decreased cellular growth rate or otherwise interferes with homeostasis, the cell’s ability to maintain a stable internal cellular environment.
1.1.2 Overcoming cellular limitations in metabolic engineering
One potential solution to the third problem is to decouple cell growth (an energy-intensive process) from resource production using a two-phase fermentation process. In the first phase, cells are allowed to grow without restrictions. In the second phase, growth processes are switched off, which frees up internal cellular resources for heterologous production while also preventing toxic byproducts of this production reaction from interfering with cell growth processes.
Many methods exist to control cell growth, but one attractive technique that has emerged is optogenetic (light-based) manipulation: yeast can be genetically engineered so that essential growth pathways are controlled by a light-activated protein. Zhao et al. successfully demonstrate that two-phase fermentation indeed allows yeast cells to switch resources from growth (under blue light) to production (in darkness) (Zhao et al. 2018). However, when light-controlled strain cultures are left in darkness/non-growth conditions for long periods of time (40-100 hours), yeast cultures eventually escape the optogenetic growth control, developing an ability to grow even in the dark (Figure 1). It is hypothesized that this is due to the emergence of “cheater” cells, cells which receive mutations to the genetic elements involved in optogenetic control (Gonzalez et al. 2025).
In this thesis, I model the population dynamics of growth-controlled cells when cheaters emerge. Using a few salient parameters, such as cell growth, death, and mutation rate, the model captures the unique features of population growth following cheater emergence: an extended lag time before cheaters arise, rapid increase in population size around t = 50 hours, and for some trials, multiple bursts of population growth
Further, I will investigate the effect of a proposed intervention on these cells–expressing a DNA-binding protein–that nearly doubles the amount of time taken for cells to cheat. By varying the parameters to match two hypotheses for how this intervention effects a change on the cell, I will obtain evidence in support of one, both, or neither of these hypotheses. This evidence will be used to inform our understanding of whether, and how, chromatin-binding proteins slow the onset of genetic instability. Insights from the model may also be used to translate the findings on chromatin-binding proteins to cells that contain gene circuits besides the growth-control circuit tested here.
Del Vecchio, D., & Murray, R. M. (2015). Biomolecular feedback systems. Princeton University Press.
González, L., Echauri, S. A. G., Jeronimo, C., Poitras, C., Gencel, M., Serohijos, A., Bloom, K., Robert, F., Avalos, J. L., & Michnick, S. W. (2025). HP1-enhanced chromatin compaction stabilizes a synthetic metabolic circuit in yeast (p. 2025.03.04.641524). bioRxiv. https://doi.org/10.1101/2025.03.04.641524
Markina, N. M., Kotlobay, A. A., & Tsarkova, A. S. (2020). Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts. Acta Naturae, 12(2), 28–39. https://doi.org/10.32607/actanaturae.10966
Radde, N., Mortensen, G. A., Bhat, D., Shah, S., Clements, J. J., Leonard, S. P., McGuffie, M. J., Mishler, D. M., & Barrick, J. E. (2024). Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology. Nature Communications, 15(1), 6242. https://doi.org/10.1038/s41467-024-50639-9
Zhao, E. M., Zhang, Y., Mehl, J., Park, H., Lalwani, M. A., Toettcher, J. E., & Avalos, J. L. (2018). Optogenetic regulation of engineered cellular metabolism for microbial chemical production. Nature, 555(7698), 683–687. https://doi.org/10.1038/nature26141
Author Commentary / Sanjana Venkatesh
I came into Princeton with a desire to understand how living systems are programmed: how do our cells ‘know’ what to do, and how can we control their behavior? My search for answers took me to far corners of the academic space on campus, and I found ideas in electrical engineering, molecular biology, neuroscience, philosophy, and more. My senior thesis brings together what could be called the ‘philosophical ideas’ of ECE–how information is stored and used, how components can be linked together into circuits that perform complex tasks–with the workings of biology, and uses a little bit of math and coding to put those ideas together.
Because of the interdisciplinary nature of my project, I felt that a strong orienting section was crucial to my thesis report. Writing this section was challenging for a couple of reasons: first, I had to take care to steer away from niche field-specific language without sounding too informal or making it seem like I was circumlocuting technical words. Second, writing conventions vary within engineering fields, with different readers seeking different information about the problem at hand. My advisors and readers are housed in three departments (MAE, CBE, and ECE), and I had to carefully choose information that would be appropriate to their respective areas of expertise while providing sufficient background about the other areas.
In this section, I aim to lay out the fields of synthetic biology and metabolic engineering in broad strokes: what are the motivating ideas and overarching goals? What experimental techniques are commonly used? What are the major challenges? A major goal for this section was to answer these questions in simple terms, distilling the fields down to only the relevant points required to understand my project, then presenting them as clearly as possible. Two pieces of the Lexicon were crucial to this: careful structuring, and deliberate use of key terms. I broke the excerpt into three sections: one outlining the motivation and goals of the field, a second describing some key problems, and a third that began to zero in on the specific setting for my thesis. I also defined terms like “mutation,” “cheater,” “stochasticity,” and “metabolic burden,” which all feature prominently later in the report. This excerpt also begins to set up the motive for my thesis, situating my project within the broader fields of synthetic biology and metabolic engineering.
One reason I felt so comfortable writing this section, and proud of it once it was finished, was that it was a summary of many of the ideas that I picked up over the course of my time here. By the time I started writing my report, I had read dozens, perhaps hundreds, of review papers, textbook chapters, and news articles on synthetic biology and metabolic engineering. This exercise better acquainted me with writing conventions across different engineering disciplines while also giving me ideas on how to structure this excerpt most logically. Beyond serving as the orienting section of my thesis, this piece is a distillation of much of my academic exploration at Princeton.
Editor Commentary / Jessica Wang
How do we explain our work to audiences outside of our discipline? Sanjana tackles this question with professional precision in her thesis project introduction. This section demonstrates what it means to write with an audience in mind — in this case, an interdisciplinary set of readers with varying backgrounds in biology and engineering.
A piece like this can easily become bogged down with confusing jargon. Yet what stands out about Sanjana’s execution is how she carefully defines key terms in digestible language. She makes liberal use of tactics such as subheadings, italicization, and list format to lend structure to her thoughts. In doing so, she is able to fit an impressive amount of information into little space without losing clarity or direction.
Her introduction is an example of the classic inverted pyramid structure: She begins broadly and narrows in on her specific corner of the field. Like a tour guide, she takes us from an overview of her discipline into the world of programmable cells, and then she delves deeper into the technique of optogenetic growth control and the problem of cheaters. She seeds motive throughout the piece using signal phrases about challenges, limitations, or unexplored problems in the field. This neatly leads us to the end, in which she presents her project’s two parts to address this research gap.
This piece shows us how to apply Lexicon concepts to a STEM research sphere. For Sanjana’s thesis, orienting means situating her project in the landscape of past scientific research. The scholarly conversation becomes a “dialogue” between past scholars, studies, and research advances. We find motive in a research gap: a puzzle, a “not obvious” corner of the field, a problem that has yet to be solved. This introduction is informative and deliberate, and Sanjana’s confident writing voice guides the reader through every step of the way.
Author
Sanjana Venkatesh ‘26 is an Electrical and Computer Engineering major pursuing minors in Bioengineering, Robotics, and Religion. She is interested in synthetic biology and bioethics and enjoys exploring these topics from various angles through different departments at Princeton. She is involved with performing arts on campus through Naacho South Asian Dance and Kalaa Dance Troupe, and loves to spend time outdoors with friends from OA and Running Club.
Editor
Jessica Wang ‘26 is an Ecology and Evolutionary Biology major who loves writing stories. Her writing has appeared in the Nassau Literary Review, figments, Arch & Arrow Literary Magazine, and the Daily Princetonian’s Prospect section. On campus, you can find her working as a Writing Fellow, singing in the Playhouse Choir, and getting distracted by birds.
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