Programs
Building open, integrated synthetic cells
Overview
We developed a prototypical open-source synthetic cell that integrates two essential synthetic cell functionsâdetection and response. This work resulted in a set of fully open and specified components, enabling the formation of Nucleus, and jumpstarting collaborative and interoperable synthetic cell engineering across the research community.
Developer Cell: A modular, extensible chassis for building synthetic cells
Overview
We developed an open-source synthetic cell (âDeveloper Cellâ) and tools to enable more capable synthetic cells to be built using Nucleus. We have released two modules (PPK and ClpXP) that operate on standard Cytosol in a standard membrane, a PURE performance landscape dataset, and a synthetic cell engineering DNA toolkit. Work is ongoing to explore additional energy modules and the SecYEG module.
Advisors
SIMBA: Simulation and Inference of Microbial Behavior and Adaptation
Overview
We are part of a DARPA initiative (SMS) to build a whole-cell simulation platform for E. coli-based biomanufacturing. b.next is advancing the model by generating high-resolution datasets using our automated platform for building defined Cytosol with varying composition. We are also building synthetic cell standards with defined molecular composition to enable single-cell E. coli mass spectrometry.
AI-Driven Cell-Free Energy Development and Optimisation
Overview
We are building a closed-loop AI scientist that autonomously designs, tests, and integrates new functional modules into Cytosol to rapidly expand synthetic cell capabilities. We have demonstrated an end-to-end workflow for development and integration of a simple energy module (PPK)âfrom AI-based hypothesis and design of experiments to automated experimental implementation, analysis, and open publishing. We are improving this workflow and testing it on a more sophisticated energy module (Glycolysis).
Partners
Developer Cells as a Scalable Platform for Predictable Engineering of (Non-Living) Biological Machines
Overview
We are serving as the technology integration and infrastructure partner for a global initiative to build integrated, reproducible, open-source synthetic cell applications. We are facilitating development and collaboration through Nucleusâour open-source platform providing shared protocols, material specifications, and digital tools. We are manufacturing key open-source and custom Cytosol reagents to ensure teams have standardized physical materials necessary for validation and integration. We are supporting integration and reproducibility at Nucleus Labs.
Partners
MetaPURE: Cell-Free Modular Systems
Overview
We are a Principal Investigator for an NSF initiative (CFIRE) to place cell-free technology on an exponential growth path and drive industry adoption. We are developing Cytosol as a foundational link for the cell-free industry between enzyme cascades and cellular lysatesâbuilding and testing new modules, technologies, and standards to enable composition, engineering, and re-use.
Partners