Jan-Hannes Schaefer

CryoSift – An accessible and automated CNN-driven tool for cryo-EM 2D class selection

Check out our new preprint from the @landerlab.bsky.social, Stagg-Lab and Cianfrocco-Lab: CryoSift - An accessible and automated CNN-driven tool for cryo-EM 2D class selection www.biorxiv.org/content/10.1...
Happy testing: cryosift.org #cryoEM #CNN

Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV Cryoelectron microscopy (cryo-EM) has transformed structural biology by providing high-resolution insights into biological macromolecules. We report s…

Now out in Structure: Paper on high-resolution #cryoEM using the 100 kV Tundra cryo-TEM by Dimple Karia, Adrian Koh, @abhaykot.bsky.social, @lingboyu.bsky.social, @landerlab.bsky.social and many others. Happy to have contributed to this effort. Check it out:
www.sciencedirect.com/science/arti...

Frontiers | Effect of Brisk Walking on Health-Related Physical Fitness Balance and Life Satisfaction Among the Elderly: A Systematic Review Background: Although the elderly frequently engages in brisk walking as a form of exercise, little has been reported in the literature about the effect of br...

Great! Quantity matters, but quality seems to be important too: Short but brisk walking for all the office folks. doi.org/10.3389/fpub...

AlphaFold - A practical guide AlphaFold - A practical guide

Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!

There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...

Yet another great case study! Maybe most symmetric assemblies are not? And helical assemblies next @structurabio.bsky.social ?

Case Study: Pseudosymmetry in TRPV5 and Calmodulin (EMPIAR-10256) | CryoSPARC Guide Processing EMPIAR-10256 with a focus on handling pseudosymmetry and 3D Classification parameter choices.

guide.cryosparc.com/processing-d...

Provocative but there is truth to it! "Every time a scientist abdicates their work to an AI tool, that is a tacit admission that the work is not worth being done by the scientist." #LLM #science

Running Phenix and stuck?
Now you can ask the new Phenix chatbot anything from the 600-page tutorial about how to run any program.
Big thanks to Tom Willinger for making this happen!
Try it out: phenix-online.org/version_docs...

Magellon GUI for cryoEM

Exited to share my first PostDoc contribution! Like Magellan explored the globe, you can explore your cryoEM data with Magellon. Congrats to all involved. Scott Stagg Lab & Michael Cianfrocco Lab @landerlab.bsky.social www.biorxiv.org/content/10.1... 🌎❄️🔬

Thanks for these suggestions. I'll have a go at implementing them.

Motion visualization with ChimeraX

Do you want to visualize motion in protein structures? I've used @chimerax.ucsf.edu and little python code to do just that github.com/schaefer-jh/.... Here is some ABC transporter magic. #LLM assisted #coding

The Breakthrough Blood Test for Alzheimer's Disease The p-Tau217 Biomarker for Prediction and Prevention

p-Tau217 is a breakthrough blood test that can predict and may help prevent Alzheimer's disease.
erictopol.substack.com/p/the-breakt...
Here's the rundown on it. Free, open-access.

Graphical abstract of Fuzzy-Inturned and Rab23 on liposomes.

New preprint. Mechanistic Plasticity of the RabGEFs Mon1-Ccz1 and Fuzzy-Inturned. Showing how TLD-RabGEFs adapt to different cellular functions. Congrats to first author @stephanwilmes.bsky.social from the Kümmel Lab. #cryoEM #openscience @arnemoeller.bsky.social doi.org/10.1101/2025...

The Shingles Vaccine and Reduction of Dementia A compelling new study adds to the body of data supporting some protection provided by the vaccine

A major paper @nature.com this week found a significant decline in dementia after an outdated Shingles vaccine.
I've reviewed the study and many other relevant ones here
erictopol.substack.com/p/the-shingl...

Our new structure of GCase-LIMP-2 provides details of an M6P-independent lysosomal transport complex, relevant for Gaucher's and Parkinson's Disease. Congrats to first author Jan Dobert from Zunke-lab & Arnold-lab @arnemoeller.bsky.social . Now out in @naturecomms.bsky.social rdcu.be/efItX #cryoEM

Read of the week. Is this future of freezing cryo-EM grids - Foam Film Vitrification without blotting? Congrats to Russo and Löwe labs!

Choose wisely! Congrats to @leahoffmann.bsky.social @anikabaier.bsky.social

Grateful for all involved in getting me here! @dfg.de @arnemoeller.bsky.social Off to new cryoEM adventures!

It cannot be done... They said. Today, we can see atoms and solve structures of macromolecules to design live changing medicines! Great job showing how science works.

YouTube video by Veritasium What if you just keep zooming in?

Seeing atoms was thought impossible. Science found a way www.youtube.com/watch?v=88bM...

The Solaris causes a partial softening of the PLA, which starts at 55 °C, causing the grids to stick. Using a Pelco did not cause this issue.

Short update. Using a Solaris, UltrAuFoil grids slightly stick to the PLA but do not show visual contamination in TEM.

Great. We are using the same filaments.

Thanks for sharing @lrouillan.bsky.social. Any suggestion on the filament material to avoid contamination during glow discharge?

Electron microscopy grid holder by _rouillac | Download free STL model | Printables.com A simple design to hold flat CryoEM grid compatible with glow discharge. | Download free 3D printable STL models

🔬 Tired of dropping CryoEM grids during manipulation? Check out my 3D-printed holder! Download the STL file here: www.printables.com/model/900940.... Compatible with glow discharge systems, it makes your workflow smoother and more efficient. 💡 #CryoEM #3DPrinting #OpenScience

A picture showing the different modules available on MyScope, these include: Microscopy Concepts, Scanning Electron Microscopy, Transmission Electron Microscopy, Light & Fluorescence Microscopy, Cryo-Electron Microscopy, X-ray Diffraction, Energy Dispersive Spectroscopy, Atom Probe Tomography, Focused Ion Beam, Scanning Probe & Atomic Force Microscopy, Secondary Ion Mass Spectrometry, Research Data Management, Work Health and Safety

Are you planning your lectures/course content for this year? Check out MyScope – our free #microscopy training website with theory, quizzes and microscope simulators 🧪

Developed by our experts, open to the global community: www.myscope.training
#openlearning

Dolphin and surfer decmber in San Diego.

Spot the dolphin.

Left, cry-EM structure of the complex between MIK2 (green), the immunoregulatory peptide SCOOP (yellow) and the LRR of the co-receptor BAK1 (white) with only the most rigid part of the N-glycans resolved (1 or 2 or none) and represented with sticks. Right, reconstruction of the N-glycosylation with plant N-glycans G90477LS,selected to be all the same as glycoproteomics data is not available (as far as I know)

If you are interested or working in #structuralbiology, as you see any protein (yes, *any*), you should be thinking: is it glycosylated? The answer is likely to be yes! You can predict N-glycosylation sites and rebuild all types of glycans with ReGlyco glycoshape.org 😌
Check out the example ⬇️ 1/2

Here is a starter pack for CryoEM/ET enthousiasts
To be completed
go.bsky.app/JmQksC