Upscaling Engineering of Synthetic Biomachines

The long-term goal of this research activity is to formulate, demonstrate, and evaluate a new model for biological systems engineering. To develop and demonstrate this approach, a team of research engineers will integrate components and circuits created by others to implement a non-trivial biological function. The demonstration will include standardizing components and chasses, “routinizing” the required workflows, and systematizing the design abstractions and tools. This project is an 18-month seed effort focused on proof-of-concept integration in synthetic cells that would yield a novel, multicomponent “biomachine”, while generating and disseminating a set of component standards, design abstractions, software tools, laboratory protocols, and open-source artifacts (hardware, software, wetware) to the community.

Current participants: b.next Additional participants: Mark Prator (Technician, EAS) Yan Zhang (Postdoc, BBE)

Collaborators (Steering Committee): Drew Endy (Stanford) Paul Freemont (Imperial) Elizabeth Strychalski/Jane Romantseva (NIST) Past participants:

Objectives

The goal of this project is to demonstrate a new model for biological systems engineering that can serve as a starting point for a larger effort in systems engineering of biological systems. We will focus on proof- of-concept demonstrations in synthetic cells, a class of non-living biological machines, constructed from biological components such as lipids, amino acids, proteins, and DNA. Synthetic cells do not mutate or evolve, allowing more systematic and repeatable engineering, and also providing significant advantages in environments where it may not be desirable to deploy genetically engineered organisms. We anticipate that the methods we develop can also serve as a testbed for engineering methods in living organisms.

Specific objectives:

• M0: Recruit lead engineer, project team, and steering committee
• M1: Define demonstration project, components/partners, and required tools
• Iterative engineering of demonstration project and release of open-Source artifacts
  • M2, 31 Dec 2023: initial attempt at integration + initial release of open source artifacts
  • M3, 31 Mar 2023: second iteration/release + proposal for Phase II activities, funding
  • M4, 30 Jun 2023: third iteration/release; stop or proceed to Phase II
  • M5, 30 Sep 2024: successful transition to FRO or other model for continued activity

References

None to date

This project is funded through Schmidt Futures.

Agency: Schmidt Sciences Grant number: 2023-3-2-1

Start date: 1 Apr 2023 End date: 30 Sep 2024

Support: 3 full-time research engineers Reporting: Interim and final report