iiinova — where your digital self keeps evolving

Travis Lee @tralee-sci.bsky.social · 22/05/2026

We also provide interactive access to at our web portal to explore expression data and TF motif activity within our single-cell and multi-modal datasets. 7/8 arabidopsisdevatlas.salk.edu

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Travis Lee @tralee-sci.bsky.social · 22/05/2026

This results in a model where positionally defined cell states bifurcate to asymmetrically regulate cell elongation to form the apical hook arch. We hypothesize that these divergent regulatory networks may be utilized broadly to regulate plant morphogenesis and bending 6/8

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Travis Lee @tralee-sci.bsky.social · 22/05/2026

Zooming in on these cells, GRN construction reveals bifurcating regulatory networks that asymmetrically drive cell elongation through hormonal regulation. As predicted by our GRN, we also rescue our mutant phenotype with exogenous GA hormone treatment 5/8

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Travis Lee @tralee-sci.bsky.social · 22/05/2026

We identify a transient cell niche below the shoot meristematic region that functions as a regulatory 'hub,' and find that mutation of TFs specifically expressed and with binding activity in these cells leads to defects in apical hook form 4/8

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Travis Lee @tralee-sci.bsky.social · 22/05/2026

Using genetic mutants and manual dissection, we find vast heterogeneity within cell types in the apical hook attributed to intersecting developmental and hormonal regulation. Our spatial datasets enable the identification of the (developmental) time and place of this regulation 3/8

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Travis Lee @tralee-sci.bsky.social · 22/05/2026

How do organisms grow an arch? In the apical hook, counter hormone gradients drive cell elongation asymmetrically; but as a standing wave cells transiently enter and exit the apical hook over a span of hours, which complicates our understanding of this structure 2/8

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Travis Lee @tralee-sci.bsky.social · 22/05/2026

How do cells break symmetry to generate new shape and form? Using the apical hook as a model, we @joeecker.bsky.social applied spatial and single-cell multiomics, and identify a regulatory hotspot in a transient cell niche that drives this U-shaped structure 1/8 bsky.app/profile/bior...

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Travis Lee @tralee-sci.bsky.social · 16/05/2026

I eagerly await the reciprocal experiment www.nature.com/articles/d41...

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Travis Lee @tralee-sci.bsky.social · 19/08/2025

We hope that this 'initial draft' of a spatially-resolved cell atlas of the Arabidopsis lifecycle will enable further biological discovery and function as a framework for future focused studies. 6/end

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Travis Lee @tralee-sci.bsky.social · 19/08/2025

We also took a deep dive investigating cell states within the compact yet complex hypocotyl apical hook where we found that our paired spatial + single-cell datasets were key for identifying novel cellular states at the intersection of development and hormonal regulation. 4/n

spatial expression of markers within the hypocotyl apical hook

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Travis Lee @tralee-sci.bsky.social · 19/08/2025

We found novel and subtle phenotypes visible to the naked eye in mutants of genes with combined cell type and developmental expression specificity. These results highlight that our dataset can guide novel discovery by knowing when and where a gene is natively expressed. 3/n

expression MIOX1 and phenotype of a miox1 mutant

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Travis Lee @tralee-sci.bsky.social · 19/08/2025

With our approach of paired single-nucleus and spatial transcriptomics to diverse Arabidopsis organs, we identified and spatially validated cases of both conserved and divergent markers of coocell types and cell states along the Arabidopsis lifecycle. 2/n

collage of single-nucleus and spatial transciptomic datasets

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Travis Lee @tralee-sci.bsky.social · 19/08/2025

Thrilled to have our spatial single-cell atlas of the Arabidopsis lifecycle in @NaturePlants. Turns out that its easy to make nice images when spatial expression of 1,000 genes is available! 1/n @natanellae.bsky.social @tatsuyanobori.bsky.social @joeecker.bsky.social www.nature.com/articles/s41...

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Travis Lee @tralee-sci.bsky.social · 19/08/2025

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Travis Lee @tralee-sci.bsky.social · 19/08/2025

spatially restricted expression of markers in the hypocotyl apical hook

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Travis Lee @tralee-sci.bsky.social · 19/08/2025

Expression and phenotype of MIOX1 and a miox1 mutant

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Travis Lee @tralee-sci.bsky.social · 19/08/2025

With our paired application of single-nucleus and spatial transcriptomics to diverse Arabidopsis organs, we identified and spatially validated cases of both conserved and divergent markers of cell types and cell states along the Arabidopsis lifecycle. 2/n

collage of single-nucleus and spatial datasets

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Travis Lee @tralee-sci.bsky.social · 12/06/2025

Graphical abstract of the year award goes to www.sciencedirect.com/science/arti...

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Travis Lee @tralee-sci.bsky.social · 11/08/2023

Can't beat the view leaving from lab

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