Link to the paper www.nature.com/articles/s41...

Plasmids for GEMINI are available at @Addgene www.addgene.org/browse/artic...
Happy to discuss applications/collaboration! Please reach out!

Huge shoutout to the Janelia Open Chemistry program led by @rhodamine110.bsky.social for developing and sharing the amazing Janelia Fluor dyes! They are essential for timestamping in GEMINI!

This work was led by my outstanding students Yuqing (Eugene) Yan and Jiaxi Lu. Many thanks to the Baker lab
@uwproteindesign.bsky.social, the Bergles lab @jhu.edu Neuroscience , and Tim Shay and the team
@caltech.edu CLOVER Center for collaborative support! [11/n]

GEMINI temporally resolves DOX-dependent transcriptional history and seizure-induced neural activity history in mouse brain, opening an exciting path toward organ-wide, cellular-resolution dynamic mapping. [10/n]

The readout is single-cell and scalable to intact tissues. In brain, each GEMINI particle can be registered to its corresponding neuron, enabling maps of cellular dynamic pathway histories across large in vivo samples—without continuous imaging. [9/n]

In vivo demo 2 (mouse brain): GEMINI also works in native tissue like the mouse brain. High-level GEMINI expression showed minimal impact on neuronal health, firing, and animal motor/cognitive functions. [8/n]

In vivo demo 1 (tumor xenograft): we implanted xenografts stably encoding GEMINI to report inflammation dynamics in mice. We achieved tumor-wide expression, and temporally resolved differential responses across cells in distinct microenvironments. [7/n]

Before deploying GEMINI in vivo, we established a systemic timestamping strategy: retro-orbital delivery of high-bioavailability Janelia Fluors generates an in vivo labeling pulse that marks the growing frontier of GEMINI, producing a sharp time-stamp band. [6/n]

Benchmarking in culture: GEMINI resolves activation and deactivation of TNFα-induced NFκB signaling with hour-level temporal resolution. Multiple events can be recorded, with dynamic features retained and decodable. [5/n]

By incorporating fiducial timestamps, cellular events are anchored to absolute time, enabling temporal decoding of dynamic histories. Signal amplitude is captured by the fluorescent intensity of the bands. [4/n]

Concept: we computationally designed a protein assembly that grows predictably within live cells into a molecular recorder that encodes cellular signals as fluorescence patterns for retrospective readout. [3/n]

Motivation: cellular signaling is dynamic and heterogeneous. Live imaging is low-throughput and limited in coverage; endpoint assays erase temporal information. We sought a scalable way to map event timing + amplitude at scale. [2/n]

🚨 Today in Nature, we report GEMINI—a genetically encoded intracellular memory device that writes cellular dynamics into tree-ring-like fluorescent patterns within cytoplasmic protein assemblies. [1/n]