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Vinay Ayyappan

@vayyappan.bsky.social
31 followers 44 following 10 posts

Penn MD/PhD student. Runner when bones work

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Reposted by Vinay Ayyappan
Alfonso Martinez Arias @amartinezarias.bsky.social · 10/10/2026
..and have a look at the highly related paper from @arjunraj.bsky.social biorxiv.org/content/10.1... with complementary experiments that reinforce the point and reveal multicellular #memory@arjunraj.bsky.social
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Reposted by Vinay Ayyappan
Alfonso Martinez Arias @amartinezarias.bsky.social · 02/05/2026
A clear/significant finding derived from the single cell (sc) analysis of biological systems has been the realization that phenotypically homogeneous populations are heterogeneous at the level of gene expression (GE). www.cell.com/fulltext/S00... 🧵
cell.com
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
Gene expression is a fundamentally stochastic process, with randomness in transcription and translation leading to cell-to-cell variations in mRNA and protein levels. This variation appears in organis...
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Reposted by Vinay Ayyappan
Alex Hughes Lab @hugheslabpenn.bsky.social · 03/04/2026
@lsprahl.bsky.social and Ronald Canlla in the lab just published a detailed study on remote-controlled epithelial budding morphogenesis. We can direct budding, tubule elongation, and perhaps branching in human kidney organoids via a light-activated RET receptor. www.biorxiv.org/content/10.6...
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Reposted by Vinay Ayyappan
Arjun Raj @arjunraj.bsky.social · 21/03/2026
One of my very favorite papers from the lab! Shows that individual cells can learn by forming memories. Amazing work by Jess Li!
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Reposted by Vinay Ayyappan
David Brückner @davidbrueckner.bsky.social · 05/01/2026
How can cells use information from neighboring cells to improve the spatial precision of morphogen patterns? 🤔 We show that cells can gain positional information by "talking" to their neighbors - how much depends critically on spatial correlations of the patterns. buff.ly/w56OUJT
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Reposted by Vinay Ayyappan
Grant Kinsler @grantkinsler.bsky.social · 18/12/2025
We designed SpaceBar to be as easy to use as possible: Cells are labeled via lentivirus transduction, and barcode detection works with any standard imaging-based spatial transcriptomics workflow. w/ Yael Heyman and @arjunraj.bsky.social Check out the thread from the preprint for more info!
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Reposted by Vinay Ayyappan
Kate Cavanaugh @katecavanaugh.bsky.social · 01/10/2025
See this? This = implanting mouse embryo. Usually this happens inside its mother and is invisible to us, but we can actually watch implantation ex vivo with the hope of understanding why implantation goes awry in embryos of older women. A 🧵...
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Reposted by Vinay Ayyappan
Cells & Development @cellsdev.bsky.social · 26/09/2025
In this intriguing paper published from the lab of @amartinezarias.bsky.social , they looked at the effects of size on morphology, tissue composition, and gene expression of gastruloid development. They found that AP elongation dynamics is size-dependent! Check it out here: doi.org/10.1016/j.cd...
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Reposted by Vinay Ayyappan
Alex Hughes Lab @hugheslabpenn.bsky.social · 22/08/2025
Aria Huang's @azyhuang.bsky.social paper is out on beautiful embryonic kidney 3D cultures that branch properly and enable live defect analysis. She also finds intriguing effects of adhesion and stiffness on explant size, shape, and nephron formation - boundary conditions matter! rdcu.be/eBSUK
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Vinay Ayyappan @vayyappan.bsky.social · 16/07/2025
@hugheslabpenn.bsky.social thank you so much!!! It’s been beyond a joy to work on it
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Vinay Ayyappan @vayyappan.bsky.social · 15/07/2025
[8/8] Huge thanks to all co-authors and the lab from whom I’ve learned so much, @arjunraj.bsky.social for so much mentorship and support. Particular shoutout to Cat, whose preprint also dropped. It’s amazing and everybody should check it out: www.biorxiv.org/content/10.1...
biorxiv.org
Single-cell spatial mapping reveals reproducible cell type organization and spatially-dependent gene expression in gastruloids
Gastruloids are three-dimensional stem-cell-based models that recapitulate key aspects of mammalian gastrulation, including formation of an anterior-posterior (AP) axis. However, we do not have detail...
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Vinay Ayyappan @vayyappan.bsky.social · 15/07/2025
[7/8] We think morphogen signaling partly governs how clones partition tasks in gastruloid development. Adding Retinoic Acid to chimeric gastruloids caused clones to mix together, and inhibiting Nodal signaling disrupted propensity, even though clones stayed separated from one another.
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Vinay Ayyappan @vayyappan.bsky.social · 15/07/2025
[6/8] We integrated our lineage-tracing with spatial transcriptomics. Pure-clone gastruloids poorly organize marker gene expression. Combined-clone gastruloids have marker gene expression that is more comparably organized to bulk gastruloids.
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Vinay Ayyappan @vayyappan.bsky.social · 15/07/2025
[5/8] Instead of each clone trying to form all tissue types, biased clones focus on what they do best, and together they collectively organize more accurately than any individual clone could achieve alone.
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Vinay Ayyappan @vayyappan.bsky.social · 15/07/2025
[4/8] We think this is a form of “division of labor” among biased clones, which specialize in forming certain tissues. Kinda like Adam Smith’s example of workers in a pin factory. Every worker CAN do any task, but is better at some than others. Divvying-up the work boosts output.
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Vinay Ayyappan @vayyappan.bsky.social · 15/07/2025
[3/8] Mixing clones together also helps gastruloids elongate properly, and again, each clone takes its preferred spot along the anterior-posterior axis, effectively partitioning the job of making the gastruloid among themselves.
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Vinay Ayyappan @vayyappan.bsky.social · 15/07/2025
[2/8] Every clone has a preferred location in the chimeric gastruloid. Some have a propensity for the anterior, some for the posterior. Here, that propensity held in nearly every gastruloid over several rounds of aggregation.
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Vinay Ayyappan @vayyappan.bsky.social · 15/07/2025
[1/8] We used a fluorescence-based lineage tracing approach to track individual clones in a polyclonal aggregate. Pure clones are worse at forming gastruloids. But crazily enough, if you mix them with the original bulk population, they do great!
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Vinay Ayyappan @vayyappan.bsky.social · 15/07/2025
[0/8] Stoked to share our work with @arjunraj.bsky.social on tissue organization in the gastruloid. We use lineage tracing and spatial transcriptomics to show that diversity among stem cell clones promotes, rather than hinders, gastruloid development: www.biorxiv.org/content/10.1...
biorxiv.org
Gastruloid patterning reflects division of labor among biased stem cell clones
Embryonic development typically requires precise coordination among cells to achieve reproducible outcomes, leading to the assumption that cellular heterogeneity must be minimized or buffered against....
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Reposted by Vinay Ayyappan
Jesse Veenvliet @jesseveenvliet.bsky.social · 15/07/2025
Excellent work indeed, but I feel in this context @adrianobolondi.bsky.social fantastic work should also be mentioned www.cell.com/developmenta...
cell.com
Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids
Bolondi, Law, et al. engineer a single-cell recorder to reconstruct progenitor dynamics within mouse stem cell-derived embryoids. They characterize the variable fates of axial progenitors as they cont...
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Reposted by Vinay Ayyappan
Alfonso Martinez Arias @amartinezarias.bsky.social · 15/07/2025
Two new preprints from the @arjunraj.bsky.social‬ on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about biorxiv.org/content/earl... biorxiv.org/content/earl...
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