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Jan-Hannes Schaefer

@jhschaef.bsky.social
460 followers 498 following 82 posts

Structural Biology to the rescue. Postdoc at Scripps Research. jhschaefer.de ❄️🔬 🎹⛳

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Jan-Hannes Schaefer @jhschaef.bsky.social · 19h
New preprint! In collaboration with the Akbey lab at UPitt, we solved the cryo-EM structure of FapB, an accessory functional amyloid in Pseudomonas biofilms. It forms a cross-β-solenoid closely related to the major fibril FapC, and the two cross-seed each other. doi.org/10.64898/202...
Blender rendering of Pseudomonas Fap system
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Jan-Hannes Schaefer @jhschaef.bsky.social · 15/09/2026
Turns out it's "A hair in the Soup." Tailocins are recurrent contaminants in ex vivo amyloid extraction. We've updated the preprint and provided actionable recommendations to avoid overinterpreting contaminants. doi.org/10.64898/202...
doi.org
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Jan-Hannes Schaefer @jhschaef.bsky.social · 08/09/2026
To resolve the 55 kDa Transthyretin, we used Docyl maltoside to overcome preferred orientation. A route established in @landerlab.bsky.social - doi.org/10.64898/202...
doi.org
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Jan-Hannes Schaefer @jhschaef.bsky.social · 08/09/2026
Congratulations to Marcus Jaeger for leading the efforts in the Kelly Lab. Thanks for including me in this exciting study.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 08/09/2026
Transthyretin doesn't exclusively unfold the way we thought. Under lysosomal pH (4-5), or with certain mutations, it takes an alternative route through a more expanded tetrameric transition state. And kinetic stabilizers work less well on it. @scripps.edu doi.org/10.1073/pnas...
Blender rendering of the diverging unfolding pathway of TTR
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bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 28/08/2026
Imaging large fields-of-view at high resolution in cryo-ET with square beam montaging www.biorxiv.org/content/10.64898/20…
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Jan-Hannes Schaefer @jhschaef.bsky.social · 13/08/2026
Thanks for highlighting our work. I hope it helps the community. Let me know if the Protocol works for you and what @cryosparc.bsky.social could improve.
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Eric Topol @erictopol.bsky.social · 06/08/2026
Against all odds, with an HHS that has defunded mRNA research programs, the FDA just approved the first mRNA flu vaccine
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Reposted by Jan-Hannes Schaefer
Jon Agirre @glycojones.bsky.social · 04/08/2026
Some questions for our structural biology community: What protocols do you think would be useful to have? Do you prefer to watch step-by-step videos, or follow written instructions? Of course, not everything has to be a video, but certain workflows are simply best documented on video #protocols
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Jan-Hannes Schaefer @jhschaef.bsky.social · 19/06/2026
Bacteriophage tails co-enrich with ex vivo amyloids from amyloidosis patients. Cryo-EM reveals Siphoviridae tail tube protein in ALys and AL amyloid extract. Do phages interact with human amyloids? @landerlab.bsky.social @nanigrotjahn.bsky.social & Kelly Lab #cryoEM #b3d doi.org/10.64898/202...
blender rendering of amyloids with phage tail tubes
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Jan-Hannes Schaefer @jhschaef.bsky.social · 09/06/2026
New paper out in @actacrystf.iucr.org! We benchmarked cryoSPARC for amyloid helical reconstruction: ease of use over RELION, but amyloid-specific development still needed & software interoperability remains a problem. @landerlab.bsky.social Kelly Lab @scripps.edu doi.org/10.1107/S205...
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Harry M. Williams @harrywilliams.bsky.social · 22/05/2026
We are pleased to release an update to this pre-print! Includes (1) proof-of-principle experiments on ultrasonic excitation during plunge vitrification, (2) cryo-ET characterisation of the effect, (3) and insights into grid/ice quality following ultrasonic excitation during vitrification.
biorxiv.org
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Jan-Hannes Schaefer @jhschaef.bsky.social · 21/05/2026
A set of three tube diameters with constant wall thickness worked quite well. Set particle diameter 2-3x the actual size for a larger cross-correlation box of the template. Thanks again @olibclarke.bsky.social
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Jan-Hannes Schaefer @jhschaef.bsky.social · 21/05/2026
Amazing. I ll give it a try.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 21/05/2026
Great ideas @olibclarke.bsky.social How would you deal with these tubes? Filament tracer is picking the edges rather than center. CryOLO worked, but a native CS solution would be more convenient.
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Eric Topol @erictopol.bsky.social · 18/05/2026
This is the kind of work, published today, that should be fully supported and prioritized at the highest level. Currently, there is no vaccine vs the Ebola Bundibugyo virus, the source of a major outbreak www.pnas.org/doi/10.1073/...
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 16/05/2026
Try this new online training game from Leandro F. Estrozi designed for newcomers in structural biology, with a focus on cryo-EM and cryo-ET map interpretation: rico.ibs.fr/helixplo...
Screenshot of online game
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Jan-Hannes Schaefer @jhschaef.bsky.social · 15/05/2026
While no SPA, for helical assemblies crYOLO with napari-boxmanager is my favorite. But for SPA, Topaz is still the most convenient.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 06/05/2026
In our new work from the Kelly, Ye & @landerlab.bsky.social , we link ATTR cardiomyopathy to microangiopathy. Increased capillary permeability exposes components of the vascular basement membrane to misfolded TTR. Work led by Joe Donnelly. #amyloidosis #cryoem #b3d doi.org/10.1161/JAHA...
TTR amyloids rendered with Blender
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Jan-Hannes Schaefer @jhschaef.bsky.social · 24/04/2026
Great idea. Thanks @weiss-lab.bsky.social for sharing the CAD files. We just ordered ours to test!
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Jan-Hannes Schaefer @jhschaef.bsky.social · 07/04/2026
I'll refer to a review from @sazanovlab.bsky.social "The more detergent, the higher the protein concentration required to reach the desired coverage." Also, the AWI acts as a concentrating layer, somewhat masking the true particle distribution in detergent free sample. doi.org/10.1016/j.is...
doi.org
Redirecting
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Jan-Hannes Schaefer @jhschaef.bsky.social · 07/04/2026
Thanks @brettcollins.bsky.social For TTR (55 kDa), cFAR did substantially improve, but views were still not fully randomized. I would still take the DM over making graphene grids.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 07/04/2026
And check out SurfACT too. Congrats! doi.org/10.64898/202...
doi.org
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Jan-Hannes Schaefer @jhschaef.bsky.social · 07/04/2026
We identified the maltoside detergent DM as an effective and easy solution to address preferred orientation in cryo-EM. Helped me switch from graphene grids. Special congrats to Maria Rafiq! @landerlab.bsky.social @nanigrotjahn.bsky.social @wisemanlab.bsky.social #cryoEM doi.org/10.64898/202...
Blender Rendering of vitrified HA trimer with DM at the air-water interface
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Sjors Scheres @sjorsscheres.bsky.social · 18/03/2026
We're excited to announce the beta-release of #RELION-5.1! 🥳 This release has important updates on our #amyloid processing pipeline, as described in this preprint: doi.org/10.64898/202... There are also some tweaks for #teamtomo. #OpenSoftwareAcceleratesScience
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Jan-Hannes Schaefer @jhschaef.bsky.social · 16/03/2026
Great to see one of my PhD projects out on bioRxiv. We report "A dual sensor regulates P-glycoproteins structural plasticity." Congrats to Michael Kamel for doing the heavy lifting from @arnemoeller.bsky.social & Urbatsch Lab. doi.org/10.64898/202... #b3d #cryoEM
ABC transporter Pgp in membrane. Blender Rendering
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Jan-Hannes Schaefer @jhschaef.bsky.social · 14/03/2026
For obvious reasons, we need a Paceometer! #endroadrage doi.org/10.1017/S193...
Pacometer vs. speedometer
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John Rubinstein @johnrubinstein.bsky.social · 06/03/2026
I've written a review on what I think is an extremely exciting direction in cryo-EM: Cryo-EM of endogenous membrane proteins in their native lipid bilayer Open access in Quarterly Reviews of Biophysics: doi.org/10.1017/S003...
Figure 1. Cryo-EM of abundant protein complexes in native membranes.Figure 2. Cryo-EM of membrane proteins in vesicles.Figure 3. 3D reconstruction of V-ATPase in native synaptic vesicle membranes.Figure 4. Generation of membrane vesicles for structure determination of proteins in their native lipid bilayer.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 27/02/2026
I can recommend this review doi.org/10.3389/fmol...
doi.org
Frontiers | Connecting the dots: deep learning-based automated model building methods in cryo-EM
The resolution revolution in single particle cryo-electron microscopy (cryo-EM) has dramatically expanded our structural knowledge of large biomolecular comp...
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ChimeraX @chimerax.ucsf.edu · 24/02/2026
The new ChimeraX CubeNTube plugin allows erasing parts of maps using cube, cylinder, and custom shapes and has undo. Created by Tamino Cairoli. Available from ChimeraX menu Tools / More Tools....
ChimeraX screenshot showing CubeNTube plugin.
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Hanjin Liu @liu-hanjin.bsky.social · 22/02/2026
Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...
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Jan-Hannes Schaefer @jhschaef.bsky.social · 11/02/2026
Thanks @olibclarke.bsky.social - still too fresh, maybe the bioRxiv link works better? www.biorxiv.org/content/10.6...
biorxiv.org
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Jan-Hannes Schaefer @jhschaef.bsky.social · 31/01/2026
Second that. Cryo-EM is still microscopy, so please include micrographs with visible particles.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 19/01/2026
Thanks, I guess we all needed this.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 17/12/2025
In our new preprint, we show how fibril-dynamics of signaling component TIRAP supports sensitive & fast sensing of endotoxin LPS. Congrats to co-lead @arthurfelker.bsky.social. @piehlerlab.bsky.social @arnemoeller.bsky.social #TLR #cryoEM #blender doi.org/10.64898/202...
Blender rendering of TLR4 in membrane and TIRAP fibrils at the plamsma membrane. Blender rendering of TLR4 in membrane and TIRAP fibrils at the plamsma membrane. View from the cytosol.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 11/12/2025
Thanks to @actacrystf.iucr.org for highlighting our smart 2D selection tool CryoSift. You can test it yourself here cryosift.org
cryosift.org
CryoSift - Cryo-EM 2D Classifier
Automated cryo-EM 2D class evaluation and sorting with AI.
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Gabriel Rocklin @grocklin.bsky.social · 19/11/2025
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
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hamid13r.bsky.social @hamid13r.bsky.social · 25/11/2025
Just installed Doppio on our Linux machine. This is awesome work making relion more accessible and easy to run. I haven't tried submitting jobs yet but it is already making our live easier! I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!
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Jan-Hannes Schaefer @jhschaef.bsky.social · 07/11/2025
CryoSift is now out @actacrystf.iucr.org doi.org/10.1107/S205... Thanks to all involved. Happy processing!
doi.org
CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection
CryoSift is a CNN-based tool that assesses the quality of 2D class averages. The incorporation of CryoSift into cryoSPARC workflows enables automated particle-stack cleaning.
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IUCrJ @iucrj.iucr.org · 28/10/2025
Lauren Alexandrescu et al.: `Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale #ElectronMicroscopy #CryoEM #TimeResolvedStudies ... #IUCr journals.iucr.org/paper?S2052252525…
journals.iucr.org
`Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale
The development of methods for low-cost time-resolved cryo-EM using an on-grid mixing strategy is described.
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Anastasia Gusach @g-anastasia.bsky.social · 22/10/2025
Excited to share a new chapter of my scientific journey in Chris Russo's group — developing a way to freeze proteins faster than they diffuse, paving the way for cryo-EM without air–water interface damage.
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Structura Biotechnology @structurabio.bsky.social · 20/10/2025
🚀 Introducing fully automated data processing for repeat-target #cryoEM. Using new tools in #CryoSPARC, it is now possible to obtain resolutions & map quality equal to or better than manual processing, with zero user intervention. Preprint: www.biorxiv.org/content/10.1...
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Jan-Hannes Schaefer @jhschaef.bsky.social · 17/10/2025
Thanks @odedrechavi.bsky.social. Even without explicit coverage of structural biology, it did a great job as Reviewer #0 on my latest preprint. Highly recommend www.qedscience.com
qedscience.com
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
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Jan-Hannes Schaefer @jhschaef.bsky.social · 05/10/2025
I'll try and keep you updated. The story continues.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 05/10/2025
@maxewilkinson.bsky.social fun little cryo-EM puzzle. I am still pushing the resolution to let ModelAngelo do its magic. My guess was either a common amyloid binder like SAP or an intermediate of Lysozyme-amyloids...
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Jan-Hannes Schaefer @jhschaef.bsky.social · 05/10/2025
Thanks @olibclarke.bsky.social I must have overlooked that one and should give it a go.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 05/10/2025
Reprocessed ALys Amyloids from EMPIAR-11785 Fändrich Lab
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Jan-Hannes Schaefer @jhschaef.bsky.social · 05/10/2025
CS workflow for easy testing: github.com/schaefer-jh/...
github.com
GitHub - schaefer-jh/CS-amyloids: Amyloid-processing with cryo-SPARC
Amyloid-processing with cryo-SPARC. Contribute to schaefer-jh/CS-amyloids development by creating an account on GitHub.
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Jan-Hannes Schaefer @jhschaef.bsky.social · 05/10/2025
Helical Reconstruction of Amyloids in cryoSPARC? We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social. Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...
Amyloid reconstructions from cryoSPARC
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Meytal Landau @meytallandau.bsky.social · 26/09/2025
‪We had a fantastic time hosting the first Functional Amyloid Meeting @ DESY! #FFFatDESY2025 #FunctionalFibrilFriends landaulabcssb.bsky.social
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