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Scott Coyle @cellraiser.bsky.social · 16/06/2026

This project was the brainchild of my brilliant graduate student @edenchang.bsky.social , who worked tirelessly to develop and explore this fascinating composite landscape. He is now a post-doc in Michael Rosen’s group continuing to explore exciting frontiers in condensate biology. So proud of him!

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

RIPPLE thus provides a non-equilibrium molecular multitool for understanding and engineering protein condensation out of equilibrium, and for exploring the spectrum of subcellular architectures that can arise when reaction-diffusion signaling and phase separation intersect.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

The logic of reaction-diffusion-condensation seems general. RDC may act locally to regulate individual structures, like the T-cell synapse or transcriptional hubs; or coordinate globally to pattern whole architectures, like carboxysomes (a la @cellforganized.bsky.social) and protist ciliary arrays.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

To gain intuition for these behaviors, we developed and share a RIPPLE-lab RDC webGL explorer that incorporates different condensation-dependent effects into a classic Gray-Scott Reaction-diffusion model.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

Importantly, RIPPLE reaction-diffusion-condensation architectures are not end-point structures. They can act as a scaffold for the recruitment of other macromolecules to expand their structure or functional capability.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

By screening a 6x6 combinatorial library of IDR sequences with RIPPLE, we generated dynamic IDR fingerprints that captures kinetic condensation constraints and miscibility effects relevant to the out-of-equilibrium, multi-phase context of living cells.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

Surprisingly, dual-IDR targeting causes a tug-of-war between co-existing phase-separated wave regions. Depending on IDR sequence, miscibility, and connection point, this can favor formation of compositionally complex dynamic emulsions; or reinforcement of persistent sub-cellular architectures.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

By systematically varying the underlying RD waveform, we reveal frequency-dependent transitions regulating dilute, condensed, and aggregated states specified by IDR sequence chemistry. The RD wave provides a control knob for tuning to a specific structural outcome across the spectrum of forms.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

Analyzing 1000s of RIPPLE configurations showed targeting IDRs to the assembling edge of a RD-wave causes condensation of the wavefront; while targeting IDRs to the trailing edge causes droplet assembly in the wake and higher-order organization into droplet-lattices, patterns, and macrostructures.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

Fusing IDRs to the RD Activator MinE, its partner ATPase MinD, or both, generates a vast array of activity-driven condensate behaviors and self-organizing subcellular architectures—ranging from oscillating droplet networks to persistent phase-separated macrostructures that pattern the cell.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

RIPPLE leverages our adaptation of the MinDE system as a programmable reaction-diffusion (RD) system in human cells. Coupling intrinsically disordered region (IDR) condensate-forming sequences to the MinDE machinery links phase separation to an ATP-driven, pattern-forming RD network.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

Reaction-diffusion signaling creates local concentration gradients that protein condensates can react to. We systematically map this composite landscape at scale in cells using RIPPLE, a synthetic system that tethers condensate-forming IDR modules to a programmable reaction-diffusion (RD) circuit.

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Scott Coyle @cellraiser.bsky.social · 16/06/2026

Sub-cellular architectures arise through integrating signaling and structure. @edenchang.bsky.social and @zjmaggiexu.bsky.social show how coupling reaction-diffusion signaling to protein condensation provides a tunable, regulatable landscape for sub-cellular structure www.biorxiv.org/content/10.6...

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Scott Coyle @cellraiser.bsky.social · 24/03/2026

Congratulations to my student Dennis Bolshakov and his coauthors @weix.us, Tommy, and @born2raisecell.bsky.social on making the cover of ACS Synthetic Biology! A great paper and an awesome cover 🥳 pubs.acs.org/doi/10.1021/...

The cover art, inspired by the classic Pink Floyd cover art from "The Dark Side of the Moon", depicts a white noise protein oscillation being filtered by a yeast expressing a specific synthetic circuit design into more precise, single-color waveforms. This visual echoes the noise-guided design strategies associated with Bolshakov et al.

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Scott Coyle @cellraiser.bsky.social · 17/12/2025

New in ACS SynBio: led by Dennis Bolshakov, we used the awesome power of yeast to define how expression levels, noise, and sequence program the dynamics of synthetic protein waves, allowing us to genetically encode new cellular timescales stable over generations! pubs.acs.org/doi/full/10....

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

Finally – there are many mysteries to still resolve for these cells. From dramatic metamorphic capabilities🤯 to prey preference and detection mechanisms 🕵️. For anyone interested in collaborating or getting their hands on these cells, these fantastic beasts culture well and we’re happy to share!

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

We couldn’t have taken this study to the next level without Omaya and Marine from team @dudinlab.bsky.social and Amy and Lauren from team @amyweeks.bsky.social . Together their talents brought the additional molecular and structural clarity we needed to model this circuit’s behavior fully.

Photographs of Omaya and Marine from the Dudin group; and Amy and Lauren from the Weeks group. Rockstars!

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

This work shines because of @zjmaggiexu.bsky.social passion for these cells. She built it all—the cultures, transcriptomes, analyses, modeling and collaborations—from scratch. I can’t begin to express how brilliant and hard-working a scientist she is (and she's 👀 for postdocs!). So proud of her 🥲

Photographs of Zhejing "Maggie" Xu, an extraordinary gifted, hard-working, and brilliant grad student who is as comfortable at the bench or IDE as she is in the field. Truly an amazing individual whose passion for suctorian, protists, and cell biology more generally is in a class all its own

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

More broadly, this circuit’s architecture provides a general control logic for organizing number and size of natural and engineered sub-cellular structures. Morphological circuits like this one can be viewed as building blocks for cell structure, analogous to network motifs and circuit topologies.

Figure showing how P. collini self-organizing single-cell morphology circuit can be re-parameterized, extended, or abstracted to apply to a range of different natural and synthetic cellular systems

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

While our model was built to describe P. collini’s trap scaling, we found that the trap geometries of other suctorian species from different niches could be modeled as re-parameterizations or extensions of this same core control logic!

Figure showing trap structure scaling configurations for diverse suctorian species.

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

From this, we built a mathematical model of a single-cell morphology circuit that captures the resource allocation and feedback that optimizes P. collini trap structure, in which deterministic growth of tentacles competing for free resources is interrupted by stochastic jumps in tentacle number.

Figure showing core control logic of P. collini cell morphology circuit and associated simulations of feeding and starvation single-cell trajectories that match experimental observations.

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

Key transcripts encoded centrin-like proteins, a frequent component of sensory/contractile structures in protists. We visualized tentacle ultrastructure by U-ExM with @dudinlab.bsky.social lab, discovering stunning tip and collar structures 🤯that add structural complexity to new tentacle formation.

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

Working with the @amyweeks.bsky.social lab, we used a combination of drug perturbation, proteomics, and sequencing experiments to delineate the cellular mechanisms that control trap structure maintenance and tentacle number. Critically, new tentacle formation required new transcription.

Figure showing a volcano plot of proteomics data for starved/unstarved P. collini cells; and a transcriptomics experiment showing waves of transcripts associated with tentacle biogenesis.

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

From single-cell feeding trajectories, we found that P. collini can adaptively remodel its trap structure towards the optimal configuration, expanding it upon capture and dismantling it during starvation. So what encodes the scaling and functional adaptation of the tentacle trap?

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

From >100,000 single-cell morphologies, we found that P. collini’s trap architecture scales anisotropically, favoring tentacle number over length. Remarkably, the observed scaling appeared to allocate available resources and organize trap geometry optimally for prey capture.

Figure showing the scaling of P. collini tentacle trap geometry, the associated "capture capacity" of the trap, and the observation that these geometries appear to be the optimal resource allocation for prey capture

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

We found that P. collini traps display a broad range of morphological configurations: tentacle numbers from 1-25; and tentacle lengths ~15-30 um. To study this variation systematically, we built a deep-learning pipeline and suctorian-viewer app that digitizes the 3D morphology of P. collini cells.

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

Cellular structure self-organizes through an interplay between internal mechanisms and external cues. The single-celled suctorian P. collini builds a trap structure to capture large prey using microtubule feeding tentacles, creating feedback between cell morphology and prey availability.

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Scott Coyle @cellraiser.bsky.social · 18/11/2025

How do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926

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Scott Coyle @cellraiser.bsky.social · 04/03/2025

Dennis and Elliott (another UW Madison UG!) created a huge value add by porting the GEO toolbox to budding yeast, helping us see the universality and transferability of the programming rules we worked out for human cells. They've got an exciting story using the power of yeast we plan to post soon!

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Scott Coyle @cellraiser.bsky.social · 04/03/2025

Maggie Xu @zjmaggiexu.bsky.social did incredible work driving the evolutionary bioinformatics, data mining and sequence analysis, This helped clarify the key structural and biochemical features that were hotspots for diversity and conservation in building up the GEO platform.

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Scott Coyle @cellraiser.bsky.social · 04/03/2025

Together the GEO framework provides a high-performance biochemical analogue to the carrier signals that power modern telecommunications. These circuits are just the beginning of what we aim to achieve with the power of protein oscillations.

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Scott Coyle @cellraiser.bsky.social · 04/03/2025

We demonstrate sensitive, real-time GEO-FM streaming of transcription and proteasomal degradation dynamics in single cells. Existing reporters can be converted into FM data streams measured in non-arbitrary units (ΔmHz) that are insensitive to photobleaching, fluorophore maturation , and intensity.

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Scott Coyle @cellraiser.bsky.social · 04/03/2025

In GEO-FM streaming circuits, we use a slow ATPase/activator pair to establish a carrier signal and use a fast activator module as an encoder. Coupling encoder levels to cellular activity drives changes in GEO frequency we track with signal processing and decode using a machine-learning model.

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Scott Coyle @cellraiser.bsky.social · 04/03/2025

Critically, multiple activator modules could be layered together to create a composite GEO where frequency can be dynamically manipulated by the relative amounts of each activator. This provided a simple strategy for building FM data encoding circuits for single cell-streaming! 5/

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Scott Coyle @cellraiser.bsky.social · 04/03/2025

Mining evolution, we found GEOs modules that could be synthetically recombined to generate faster or slower frequencies, akin to different color FPs. We characterized 169 GEO pairs in both human and yeast cells to develop a comprehensive platform for waveform programming across diverse eukaryotes

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Scott Coyle @cellraiser.bsky.social · 04/03/2025

GEOs are constructed from evolutionarily diverse MinDE-family ATPase and activator modules that generate fast synthetic protein oscillations when co-expressed in human cells. These serve single-cell carrier signals, with frequency and amplitude controlled by GEO component levels and activity

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Scott Coyle @cellraiser.bsky.social · 04/03/2025

FM encoding is powerful as its measured in real units (ΔHz) that are robust against fluctuating intensity and consistent b/t instruments. By assigning different frequencies to senders, multiple parallel streams can be transmitted and unmixed. GEOs unlock these capabilities for single-cell imaging

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Scott Coyle @cellraiser.bsky.social · 04/03/2025

Excited to share a new preprint! Wireless devices use FM modulation to transmit multiplexed noise-resistant data. Led by @born2raisecell.bsky.social, we create a biochemical analogue of this paradigm using genetically encoded oscillators (GEOs) for single-cell FM streaming tinyurl.com/nbs8rw42 🧵

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