In v0.3.0 we are releasing the aTc IV-HSL Responder Cell, our first instance of archetypal Responder Cells. This responder cell can detect anhydrotetracycline (aTc), a commonly used inducer molecule in molecular biology, and emit isovaleryl-l-homoserine lactone (IV-HSL), a quorum sensing module from the soybean symbiont Bradyrhizobium japonicum (Lindemann et al. 2011).

We are also releasing a Developer Note that proposes to extend the set of proteins included in PURE to improve activity and robustness. For details, read An Unexpected Enzyme in PURE: Why Folinic Acid Needs Extra Help (Ku, Y. 2025).

New to v0.3.0

Synthetic Cell

• Introduces Responder Cells, a place to represent information on a new archetype of synthetic cell that integrates detector modules (Detector Cells) with emitter modules (Emitter Cells).
• Publishes aTc IV-HSL Responder Cell, a specific instance of Responder Cell that can detect anhydrotetracycline (aTc) and emit isovaleryl-l-homoserine lactone (IV-HSL). Also publishes Protocol: aTc IV-HSL Responder Cell, which details how to prepare this cell.

Content

• Publishes aTc→IV-HSL Responder Module, the DNA module which integrates the 🟤TetR Inducible Module and the IV-HSL Emitter Module to create a system that detects aTc and and emits IV-HSL. Used in the aTc IV-HSL Responder Cell.

Cytosol

• Publishes An Unexpected Enzyme in PURE: Why Folinic Acid Needs Extra Help (Ku, Y. 2025), a Developer Note on a component in Energy Mix (folinic acid) that requires chemical conversion to be used effectively in PURE. This note reports an enzyme that can perform this conversion in situ and proposes it be added to Protein Mix to improve performance and robustness.
• Publishes Make tRNAs, a protocol for purifying E. coli Total tRNAs from MRE600 biomass.
• Updates Make Energy Mix to highlight folinic acid preparations.
• Updates Cytosol Documentation - Nucleus PURE Design Specification to show v0.3 specifications and performance data for Protein Mix and Energy Mix.
• Updates PURE Protocols for copy edits and clarity.

Development

• No updates in this release.

Community

• Publishes 🔓Open science, representing the official policies and recommendations of b.next on sharing information (DNA, methods and protocols, data, and other information) on Nucleus as of March 12, 2025.
• Publishes Cx43 Cell , reporting on a channel protein can be used as a safer alternative to ⏺️Alpha hemolysin (thank you Ahmed!)

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.

• [Dev] Make Ribosomes will publish a protocol for purifying E. coli Ribosomes from A19 biomass, using Hydrophobic Interaction Chromatography (HIC) and Ultracentrifugation on a Sucrose cushion buffer.

More Information

• To ask questions or participate in the development of Nucleus, join our nucleus-discuss mailing list.