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Mary Mirvis @marymirvis.bsky.social · 13/05/2026

11/13 When vac and nuc bending energies match, the effect of vac size on nuc morphology is partially recapitulated, but when the vac is more rigid than the nuc, these simple physical interactions are able to recreate our SXT results - the nucleus loses size scaling & is displaced and flattened.

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Mary Mirvis @marymirvis.bsky.social · 13/05/2026

10/13 But when push comes to shove, what determines which organelle squishes the other? Honor Akenuwa & Chris Lee (UCSD) built a 2D model demonstrating a range of equilibrium morphologies as a minimization of osmotic pressure and mechanical parameters setting organelle size and shape.

Simulation diagram showing the physical parameters of nucleus, vacuole, and cell

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Mary Mirvis @marymirvis.bsky.social · 13/05/2026

8/ This showed a few things. 1. size scaling is the biggest contributor. 2. vac/nuc size, position, & shape co-vary. Shape effects are stronger in large-vac cells. 3. shape variation is related to organelle position relative to cell axes. What do you see? (top 5 PCs, pink-N, grn-V. L-R: X,Y,Z)

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Mary Mirvis @marymirvis.bsky.social · 13/05/2026

7/13 We adapted the @alleninstitute.org integrated modeling pipeline to model cell, nucleus, and vacuole shapes using spherical harmonics and represent their joint variation in a 5C PCA shape space, showing which features co-vary & contribute most to variance in the dataset

Schematic of integrated shape modeling strategy

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Mary Mirvis @marymirvis.bsky.social · 13/05/2026

6/13 It appears that the degree of vacuole expansion drives progressive effects on the nucleus - at lower levels it breaks nucleocytoplasmic size scaling and displaces the nucleus toward the cell periphery, and at high levels we start to see effects on nuclear shape.

Gallery of cells of increasing Vacuole:Cell volume ratio

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Mary Mirvis @marymirvis.bsky.social · 13/05/2026

5/13 What determines this "shape competition"? Lack of surrounding space, intrinsic mechanical properties, or maybe both? we look at normal cells & some with enlarged vacuole. When the vacuole dominates the cellular space, what happens to other organelles in response, like the nucleus?

Examples of vacuole enlargement from Gary et al 1998, Iossifides et al 1980, Larson et al 2024

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Mary Mirvis @marymirvis.bsky.social · 13/05/2026

4/13 Now, we zero in on the mesoscale vacuole-nucleus interaction. The 2 largest organelles are linked by the NVJ and interact in many processes. But if you just look at their shapes, there's something else going on - sometimes the vac is indented at interface, sometimes the nuc is deformed.

3D images of vacuole and nucleus in yeast from Larabell & Le Gros 2004 and Perktold et al 2007

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Mary Mirvis @marymirvis.bsky.social · 13/05/2026

3/13 Last year, we published the largest-yet SXT whole-cell yeast dataset w/ the Larabell group- 490 cells at 30nm isotropic resolution, multiple organelles auto-segmented & tools for quant morphological analysis - OG bluetorial bsky.app/profile/wall... & paper in MBoC doi:10.1091/mbc.E24-10-0486

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Mary Mirvis @marymirvis.bsky.social · 13/05/2026

2/13 A nice model system for this geometric question is budding yeast - simple rigid shape, easy to synchronize, and amenable to whole-cell imaging and reconstruction with high throughput.

whole-cell reconstruction of budding yeast Uchida et al 2011, Wei et al 2012, and Kichuk et al 2024

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Mary Mirvis @marymirvis.bsky.social · 13/05/2026

1/13 So excited to share our new preprint!! How do organelles pack together in a crowded cytoplasm? we know organelles interact via contact sites, but how does competition for space contribute to organelle morphology and interactions? @wallaceucsf.bsky.social www.biorxiv.org/content/10.6...

Images of packed cellular interiors from Maritan et al 2022 and Heinrich et al 2021.

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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

Our corpus includes 89 studies published bw 2004-2024 screened from >11000 Pubmed results: nearly 1700 individual cells, 118 distinct datasets in 80 cell types using 13 volumetric imaging modalities, 71 comparative conditions, and at least 12 types of quantitative analyses. 5/11

overview of study: 89 studies, 118 datasets, 1689+ cells, 58 organelle combos, 13 imaging modalities, 12+ quantitative metrics, 80 cell types, 71 comparative conditions

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Mary Mirvis @marymirvis.bsky.social · 19/04/2025

To be included, studies had to show images and/or report measurements taken from complete single-cell reconstructions containing at least two clearly marked organelles in a eukaryotic system. 4/11

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Mary Mirvis @marymirvis.bsky.social · 06/12/2024

12/ It's inspired me to think deeply about the role thoughtfully-facilitated dialogues do, and can potentially, help drive interdisciplinary biology. A collaborative article describing the outcome of our discussions is in the works. In the meantime, hope to see you in San Diego!! ✨🦠🎤🔬

Word cloud of interdisciplinary terms created by participants of CCC building in vitro organelle interactions symposium

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Mary Mirvis @marymirvis.bsky.social · 06/12/2024

And our exciting lineup of talks:

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Mary Mirvis @marymirvis.bsky.social · 06/12/2024

12/ It's inspired me to think deeply about how well-facilitated dialogues do, and can potentially, have help drive interdisciplinary science. A collaborative article describing the outcome of our discussions is in the works. In the meantime, hope to see you in San Diego!! ✨🦠🎤🔬

word cloud of interdisciplinary terms created by participants of the 2023 CCC symposium

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Mary Mirvis @marymirvis.bsky.social · 06/12/2024

Oof, that didn't come out well, here's the corrected diagram

corrected Biorender-based schematic from 2023 CCC Symposium
Building in vitro organelle interactions systems: bridging cell and synthetic biology

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Mary Mirvis @marymirvis.bsky.social · 06/12/2024

10/ With the guidance of the amazing historian & philosopher of science Jane Maienschein we succeeded in pinpointing diverse motivations across fields and highlighting recent technical innovations and promising new approaches #philsci #hps centerforcellularconstruction.org/2023-ccc-sym...

Biorender-based schematic from 2023 CCC Symposium
Building in vitro organelle interactions systems: bridging cell and synthetic biology

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Mary Mirvis @marymirvis.bsky.social · 06/12/2024

2/ Early in my postdoc I idly wondered if it would be possible to learn how organelles interact and self-organize via an in vitro approach, something like this schematic: purifying organelles, encapsulating them in some sort of compartment, and fusing the compartments in a variety of combinations.

Biorender-assisted schematic from 2022 CCC Symposium
Reconstitution of Organelle Interactions: Towards
Synthetic Cell Biology

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Mary Mirvis @marymirvis.bsky.social · 06/12/2024

Find me at #cellbio2024: Part 1 I'm so excited to co-run our subgroup Toward Building in vitro organelle interactions w/ GW Gant Luxton and Hanaa Hariri !! 😀 Sat 12/14, 9:30-11am, Rm 33B. A little backstory to this unusual topic: 1/

Screenshot description of ASCB|EMBO CellBio2024 subgroup: Toward Building in vitro Organelle Interaction Systems

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Mary Mirvis @marymirvis.bsky.social · 23/11/2024

I use Blender to render whole cell volumes from tomography data! @gavsturm.bsky.social should be here too 🙂

Yeast cell mesh containing vacuole, nucleus, and lipid droplets

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Mary Mirvis @marymirvis.bsky.social · 14/11/2024

In case you need proof that there still is good in this world 😂

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