(4cf) Enabling Biology-By-Design: Bottom-up Construction of Synthetic Biosystems with in Vitro Expression Platform and Recoded Genome for Human Health

The field of synthetic biology seeks to re-engineer natural parts and pathways for impactful applications in living therapeutics, controlled environmental release and remediation, and sustainable biomanufacturing. Yet, most synthetic biology designs to date are templated in organisms selected by natural selection, not rational design. The irreconcilable differences between nature’s goal to survive and adapt and the engineer’s goal to execute designed functions often lead to mutations and loss of function.

I believe that, by pivoting away from the current paradigm of engineering biology (modifying existing biological systems to achieve desired functions) to biology-by-design (creating biological systems from the ground up with defined functions), we can unlock the breakthrough capability to realize synthetic biology’s full potential. This is my research vision, and my lab will attain this vision using three approaches:

• Assemble: Develop in vitro expression platforms to execute biological designs outside the constraints set by living cells.
• Modularize: Recode complex natural genomes to create adaptive genomes compatible with interchangeable parts and predictive design.
• Synthesize: Integrate and validate designed biosystems to deliver synthetic biosystems meeting the design specifications.

Working toward this vision, my lab will first focus on developing synthetic bacteriophages. Bacteriophages are viruses that specifically infect bacteria and offer both simplicity and complexity – with the simplest bacteriophage encoding just four genes and the most complex encoding up to a thousand genes. Moreover, the urgency of antibiotic resistance has revived interest in phage therapy for treating pathogenic infections. Recent discoveries about phage-microbe interactions in the human gut microbiome further underscore the potential for designing phages to modulate microbiome composition and function.

Taken together, my lab aims to unlock the transformative potential of biology by design, beginning with bacteriophages. This work can pave the way for innovations in medicine and microbial community control, contributing to human health and beyond.

Research Experiences:

During my doctoral research in the Styczynski Lab at Georgia Tech, I worked with lysate-based cell-free gene expression systems to construct biosensors and integrate them with new materials, such as polymer liquid-liquid phase separation and personal glucose monitors. These integrations advanced point-of-care biosensor diagnostics by enabling multiplexed analyte detection and numerical analyte quantification. Specifically, my Ph.D. work led to the development of a custom diagnostic chip with phase-separated biosensors for reporting complex analyte profiles, a colorimetric “litmus test” to assess serum micronutrient levels, and a numerical analyte quantification strategy linking biosensor outputs to personal glucose monitors.

In developing lysate-based cell-free biosensors, I discovered that crude lysate has a highly active endogenous metabolism that drains resources from the intended central reactions. This often led to unforeseen challenges in biosensor development and their integration with new materials. This challenge motivated my postdoctoral research in the Murray Lab at Caltech, where I pivoted to working with a minimal and defined in vitro gene expression system, the One-Pot PURE System, made using a co-culture of cells expressing 36 core proteins to support transcription and translation reactions.

In troubleshooting the One-Pot PURE System to achieve the same gene expression capacity as the commercial PURE systems, I uncovered multiple factors influencing gene expression capacity. These factors include offsets in critical protein and biochemical building block compositions, competition between transcription and translation reactions for energy resources, and the presence of host background protein contaminants. Building upon these insights, I am collaborating on a computational project to build a predictive model for optimizing reactions toward any protein. I am also mentoring a summer undergraduate research project to create a purer One-Pot PURE System to build a well-defined system for gene expression.

Working toward my future research vision, I secured a pilot grant from the Caltech Center of Environmental Microbial Interactions (CEMI) to use E. coli cell-free expression systems as a platform to express non-E. coli bacteriophages. The preliminary data obtained has led to a K99/R00 submission (result pending) and a collaborative R21 submission with Caltech faculty members (Prof. William Clemons and Prof. Kaihang Wang).

Teaching and Mentoring Philosophy

Educators have the power to transform students’ careers. My career trajectory was transformed by dedicated mentors who prioritized my development as a scientist. This personal experience shaped my commitment to quality teaching and mentorship. I believe that when the goal of education is centered on ownership, students become self-motivated, and progress naturally follows.

I have mentored five undergraduate students in research at Georgia Tech and Caltech. At the beginning of each project, I set clear expectations and align the project's and the student's goals. By elucidating how each step in the project contributes to the student’s goals and the overarching research goal, students are driven to take ownership of the project.

Additionally, I am actively involved in the international Genetically Engineered Machines (iGEM) community. To date, I have mentored a women-majority high school iGEM team in Lambert, GA, guiding them through the competition. I have also been an external mentor to three collegiate iGEM teams (University of Maryland, Zhejiang University of Technology, and Federal University of Rio de Janeiro), helping them with biosensor design and troubleshooting experiments. My mentorship efforts have been recognized with the Most Dedicated Mentor Award from the iGEM community.

In my teaching experiences, I have taught classes in Transport Phenomena (co-instructor), Numerical Methods (teaching assistant), and Chemical Process Design and Economics (teaching assistant). As a co-instructor and guest lecturer, I employ active, project-based learning in the classroom. I ask students to use their background knowledge to identify and categorize variables before deriving the governing equations in class. As a teaching assistant, I practice “think-pair-share” during office hours to give students opportunities to assess and practice their learning mastery with peers.

As a chemical engineering faculty candidate, I am enthusiastic about teaching undergraduate classes in numerical methods, chemical kinetics, and transport phenomena. Additionally, I am interested in teaching graduate classes in biomolecular engineering as well as developing new courses in synthetic biosystems design and virus-based technologies.

Selected Fellowships and Awards

• Caltech Center for Environmental Microbial Interactions Pilot Grant (2023)
• Caltech Presidential Postdoctoral Fellowship (2022-2024)
• MIT Rising Stars in Chemical Engineering (2022)
• Best Ph.D. Thesis Award, Georgia Tech Chapter of Sigma Xi (2022)
• First Place, Georgia Tech F. L. Suddath Fellowship Award (2022)
• iGEM Community Most Dedicated Mentor Award (2021)

Selected Publications

• Zhang, Y., Qiu, Y. Deveikis, M., Martinez, Z.A., Chou, T., Freemont, P.S, Murray, R. M. (BioRxiv preprint) Optimizing protein expression in One-Pot PURE systems: insights into reaction composition and translation efficiency. [link]
• Zhang, Y., Kojima, T., Kim, G. A., McNerney, M. P., Takayama, S., & Styczynski, M. P. (2021). Protocell Arrays for Simultaneous Detection of Diverse Analytes. Nat Commun, 12(1), 5724. [link]
• Zhang, Y., Steppe, P. L., Kazman, M. W., & Styczynski, M. P. (2021). Point-of-Care Analyte Quantification and Digital Readout via Lysate-Based Cell-Free Biosensors Interfaced with Personal Glucose Monitors. ACS Synth Biol, 10(11), 2862-2869. [link]
• McSweeney, M. A., Zhang, Y., Styczynski, M. P. (2023). Short Activators and Repressors of RNA Toehold Switches. ACS Synth Biol, 12(3), 681-688. [link]

More details about my professional portfolio and CV can be found [here]