How do organelles fit together inside a crowded cell? Answering this question requires a way to image many organelles in a whole cell at high resolution with high throughput. Our new preprint shows how to do this in yeast using soft x-ray tomography www.biorxiv.org/content/10.1... - ThreadSky

wallaceucsf.bsky.social • 193 days ago

How do organelles fit together inside a crowded cell? Answering this question requires a way to image many organelles in a whole cell at high resolution with high throughput. Our new preprint shows how to do this in yeast using soft x-ray tomography
https://www.biorxiv.org/content/10.1101/2024.10.31.621371v1

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marymirvis.bsky.social•193 days ago

Thanks for posting this Wallace! Could you quote-post or something w my handle so interested folks can follow me/I can follow them?

nehaghosh.bsky.social•168 days ago

What a fantastic question to answer! Congratulations to all the authors 👏

cellarchlab.com•193 days ago

Awesome, Wallace! But please don't forget to also harness the awesome power of chlamy genetics + reproducible cellular architecture. The changes chloro-mito morphology and interactions would be especially cool to quantify. See this recent work by the Grossman lab:
https://www.pnas.org/doi/10.1073/pnas.2407548121

wallaceucsf.bsky.social•192 days ago

Yeah!!!!! I agree this would be a killer app!!

cslamo.bsky.social•193 days ago

📌

gautamdey.bsky.social•193 days ago

This is super fun Wallace! I’d argue though that you can also get a lot of this information from U-ExM with pan-labelling or lipid staining, at comparable or better throughput. Slightly harder to do the isotropic imaging but not impossible. I’d be interested in a head to head comparison actually!

marymirvis.bsky.social•193 days ago

Thanks Gautam! Do you know of whole-cell multi-organelle reconstructions with U-ExM? I’m actually working on a direct comparison across modalities now and haven’t come across this yet

gautamdey.bsky.social•193 days ago

No it hasn’t really been done, as far as I’m aware… but it should be 😉

Happy to help! Let us know

wallaceucsf.bsky.social•193 days ago

Yeah that might be true!

ewerslab.bsky.social•169 days ago

Beautiful work! Thank you for citing us.

wallaceucsf.bsky.social•193 days ago

Our interest in such "cell anatomy" questions is inspired by published examples which clearly show that cells are jam-packed with organelles, raising the obvious (to us) question of how the steric packing of organelles might affect their size, shape, and membrane contacts

marymirvis.bsky.social•193 days ago

Refs for these images:
A. O. tauri. Henderson et al. 2007 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000749
B. S. rosetta. Laundon et al. 2019 https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000226
C. Allen Integrated Cell https://www.allencell.org/allen-integrated-cell.html

wallaceucsf.bsky.social•193 days ago

Light microscopy methods have limited resolution especially in Z, and require labels for each organelle. CryoEM tomography has a limited field of view, and its higher resolution is actually overkill. 雷公打豆腐. Serial block face would work but it's throughput is low.

wallaceucsf.bsky.social•193 days ago

many of these methods also require either laborious strain construction to introduce labels, or laborious sample preparation like fixation and embedding. all that makes it harder to look at lots of samples.

wallaceucsf.bsky.social•193 days ago

With Soft x-ray tomography you can take your yeast culture, put it in a capillary, freeze it, and then stick in the device. It collects completely isotropic images with resolution of 30-60 nm. You get multiple cells in one data collection. And you can see all or most organelles

wallaceucsf.bsky.social•193 days ago

With these obvious advantages, why hasn't soft x-ray become more popular? The issue is that while the image data has information about many organelles, extracting that information requires segmentation, which has required manual intervention.

wallaceucsf.bsky.social•193 days ago

In our new preprint, we collected enough images of yeast cells to train a CNN which now allows automated segmentation of key organelles. So now all you have to do is put your samples in a tube, get the images, and the computer produces a segmented output.

christophstc.bsky.social•193 days ago

in good company 🙂

https://schaechter.asmblog.org/schaechter/2015/02/pictures-considered-24-ostreococcus-tauri-the-smallest-known-eukaryote.html

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