In v0.2.1 we are releasing the IV-HSL Emitter Cell, an Emitter Cell which enzymatically produces an acyl-homoserine lactone (IV-HSL) and releases it into the surrounding environment. The Emitter Cell demonstrates bioproduction of a small molecule within a synthetic cell and communication with E. coli cells in co-culture. The Emitter Cell also sets the stage for our upcoming Responder Cell, which will use modules and methods developed for the Detector and Emitter cells in order to receive signals from other synthetic cells and perform signal amplification for molecule detection.

New to v0.2.1

Synthetic Cell

• Publishes the IV-HSL Emitter Cell, with performance data, usage information, and a protocol for constructing the cell itself (Protocol: IV-HSL Emitter Module).

Content

• Publishes the IV-HSL Emitter Module, the DNA module which expresses BjaI within PURE to produce IV-HSL from its substrate molecules IV-CoA and SAM.
• Updates to the DNA Distribution to include information on the Emitter Cell module components and updated PURE protein component constructs (in particular, variant sequences of ArgRS, LeuRS, IF2, and T7RNAP, which we were unable to synthesize for the initial DNA distribution or expressed poorly). We are currently preparing the new DNA distribution plates, and the open-source DNA will be available soon.

Cytosol

• Updates Make Amino Acid Mix:
• Includes new interactive worksheet that helps calculate resuspension volumes for each amino acid stock as well as volumes of each stock needed in the final amino acid mix.
• Updates language in protocol page for clarity.
• Includes new interactive worksheet in Make Energy Mix that helps calculate the volumes needed of each stock concentration in the final energy mix.

Development

• No updates in this release.

Community

• b.next engaged the iGEM community at the 2024 Jamboree in Paris. We presented Nucleus as a framework for collaboration to build synthetic cells and participated on the panel “Engineering with Openness: Advancing Synthetic Biology through Open Technologies”.

Container

• No updates in this release.

In Development

We are actively developing the following features. They are intended to be fully released in a future release. Keep up to date on the current status of these features by joining our mailing list at bnext.bio/build.

• We have performed a significant overhaul of our kinetics analysis toolbox, integrating it into a coherent Nucleus CDK python package. We are currently alpha-testing the new CDK, and expect to release it shortly on Git and through the python package manager pip.
• We are testing a new platform for publishing Developer Notes and other short-form publications that leverages the work of open-source scientific programming communities. These publications will include interactive plots, data content, and the ability to easily replicate the work performed in the publication. Watch this space.

More Information

• Code and DNA designs are available on Github.
• To ask questions or participate in the development of Nucleus, join our nucleus-discuss mailing list.