Benedikt Wimmer

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)

- 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.

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)

- 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.

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

(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.

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

(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.

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:

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

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:

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

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: