Samantha Fallacaro in the @mirlab.bsky.social defends her thesis tomorrow!
4/🧵 In addition to simulating 3D time lapse movies, SPARK can also be used to render super-resolution data for comparison to published work. Image below shows a simulation of Sox2 clustering in mESCs
3/🧵 SPARK recapitulates the clustering of transcription factors like Dorsal and Bicoid in Drosophila embryos, and Sox2 in mouse ES cells, despite explicitly excluding protein-protein interactions. (Dorsal clusters shown below)
Video
1/🧵 Can transcription factor condensate formation be explained without phase separation? Our new preprint introduces SPARK, a simulation tool that reproduces condensate behavior (clustering, fusion, FRAP) from diffusion & binding kinetics alone. Movie: 60 sec FRAP sim www.biorxiv.org/content/10.6...
7/🧵 We hope SPARK will allow users to assess whether the clusters they observe can be explained by DNA binding and diffusion kinetics, rather than higher-order phenomena like condensate formation.
5/🧵 To demonstrate that simulated data can recapitulate key emergent condensate properties we show that clusters arising from DNA binding can show fluorescence recovery after photobleaching at similar timescales as those reported for condensates. We also observe cluster fusion in simulated movies.
8/🧵 SPARK was developed by @pennengineering.bsky.social bioengineering graduate student Manya Kapoor @manyakapoor.bsky.social and inspired by our recent experimental results on Pol II (www.nature.com/articles/s41...) and Dorsal clustering (www.biorxiv.org/content/10.1...)