All this and many more changes you can find in the published version here - in my (biased) opinion, it is worth a re-read even if you have seen the preprint!
www.nature.com/articles/s41...

And of course, all was only possible thanks to our great collaboration with @mizrahilab.bsky.social

(4/4)

- We modelled the active sites of two substrate-specific amylosome enzymes and compared it to the bifunctional Amy16, to derive a structural hypothesis for the observed promiscuity.

- In collaboration with the Zeeman lab @ethz.ch we further characterized the products released by Amy16, a key enzyme in RS degradation. This revealed that Amy16 is a true bifunctional amylase and pullulanase, hydrolyzing both α(1,4)- and α(1,6)-linkages - supporting its key role in RS degradation.

- We modelled all amylosome proteins detected in our proteomics sample using AlphaFold3 and built a model of amylosome distribution around the cell wall, matching nicely the densities we observed using cryo-ET.

I'm very happy that the peer-reviewed version of our work on the amazing amylosome is now out in @natcomms.nature.com

Through the review process, we could refine our manuscript in several important areas, for example: (1/4)

Segmented filamentous bacteria undergo a structural transition at their adhesive tip during unicellular to filament development https://www.biorxiv.org/content/10.1101/2025.04.09.647586v1

Thanks Marten! With pytom-match-pick, getting the ribosome average ready for the rendering was a breeze! :)

(5/5)
It was a particular pleasure to work with a multi-disciplinary and international team on this project, from the University of Zurich, Ben-Gurion University in Beer-Sheva and the University of Greifswald!

(4/5)
By combining in-situ #cryoet and #proteomics, we could assemble an integrative model, which illustrates the remarkable architecture of the amylosome - the complex that allows R. bromii to act as keystone degrader in the gut microbiome.

(3/5)
We wanted to understand, why it makes such a complicated assembly, and found through structural and biochemical analysis that two key enzymes act synergistically if they are bound in amylosome-like complexes. #proteomics revealed that this complex is enriched when needed.

(2/5)
Our gut microbiome is essential for our health, and it relies on dietary fiber to thrive. The nutrients in dietary fiber, however, are very hard to access. Only few bacterial species manage to do so!
Our subject, R. bromii, is one of them - by using an extracellular assembly called amylosome.

Check out part 2 of my PhD work out now on bioRxiv, in which we explore an amazing protein machinery from the human gut microbiome, the Ruminococcus bromii amylosome.

A short explainer below (1/5).

www.biorxiv.org/content/10.1...

#microbiology #microbiome #teamtomo

We're running a monthly lab sustainability challenge for labs at @ethzurich.bsky.social and UZH - join in to complete 10-minute challenges to make your lab more sustainable! uzh.us3.list-manage.com/subscribe?u=...

You can find the plugin on napari-hub here: www.napari-hub.org/plugins/napa...
and the GitHub repository here: github.com/bwmr/napari-...

... which can then be written out as binary masks in the mrc format and visualized or used however you like:

... and allows you to easily create labels containing only the IDs of interest.

"napari-segselect" automatically opens the "*_segmented.mrc" files from membrain-seg as a label field...

If you want to split them up into individual segmentations, to assign different colors, or create masks for further processing, etc., membrain-seg has the flag "--store-connected-components", which assigns each connected volume a unique ID.

Hey #teamtomo, if you often find yourself using the excellent membrain-seg from @lorenzlamm.bsky.social et al., you might find my napari plugin "napari-segselect" useful. Let's say your tomogram contains the edges of two bacterial cells, each with a membrane and cell wall: