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Benedikt Wimmer

@bwmr.net

137 followers 166 following 18 posts

Using cryo-ET and timelapse microscopy to study bacteria and how they help and hurt us. PostDoc at the Jacobs-Wagner lab in Stanford. Previously at the Medalia Lab (Zurich) and Chlanda lab (Heidelberg). github.com/bwmr

Posts Replies Media

Benedikt Wimmer @bwmr.net · 25/02/2026

It‘s nice to be back to the world of #cryoET

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Benedikt Wimmer @bwmr.net · 01/12/2025

- 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.

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Benedikt Wimmer @bwmr.net · 01/12/2025

- 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.

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Benedikt Wimmer @bwmr.net · 01/12/2025

- 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.

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Benedikt Wimmer @bwmr.net · 03/04/2025

(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.

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Benedikt Wimmer @bwmr.net · 06/02/2025

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

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Benedikt Wimmer @bwmr.net · 06/02/2025

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

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Benedikt Wimmer @bwmr.net · 06/02/2025

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

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Benedikt Wimmer @bwmr.net · 06/02/2025

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:

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