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Jan Philipp Kreysing @jpkreysing.bsky.social · Aug 23

More great cryo-ET benchmarking work from my colleagues Maarten Tuijtel, Tomáš Majtner, Beata Turoňová, & @becklab.bsky.social: Systematic study of how tilt increment choice affects downstream TM & STA. Preprint has the optimally balanced tilt increment. #TeamTomo www.biorxiv.org/content/10.1...

Optimal tilt-increment for cryo-ET

Cryo-electron tomography (cryo-ET) enables high-resolution, three-dimensional imaging of cellular structures in their native, frozen state. However, image quality is limited by a trade-off between ang...

www.biorxiv.org

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Reposted by Jan Philipp Kreysing

Max Planck Institute of Biophysics @mpibp.bsky.social · Aug 18

We’re hosting the @embo.org Practical Course on In-situ structural biology by CryoFIB and CryoET in April 2026! 🧬❄️ You can expect hands-on training, cutting-edge methods, and a chance to work alongside leading experts in structural biology. 🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...

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Reposted by Jan Philipp Kreysing

Max Planck Institute of Biophysics @mpibp.bsky.social · Jul 25

AI for Cryo-ET 🌟 Our new paper presents a deep-learning framework that cleans up faulty tilt series in a more automated, precise and powerful way! 💪 Read more here: www.sciencedirect.com/science/arti...

Automated removal of corrupted tilts in cryo-electron tomography

Cryo-electron tomography (cryo-ET) enables the visualization of macromolecular structures in their near-native cellular environment. However, acquired…

www.sciencedirect.com

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Jan Philipp Kreysing @jpkreysing.bsky.social · Jul 23

New from my colleagues Markus Schreiber & Beata Turoňová: TANGO, an #opensource tool for more holistic spatial analysis of cryo-ET particles. It can clean or cluster particles, analyze lattices, and identify patterns. #TeamTomo
www.biorxiv.org/content/10.1...

Twist and Scout: Analysis and Curation of Particles in Cryo-Electron Tomography Using TANGO

Cryo-electron tomography (cryo-ET) enables the visualization of cellular structures in near-native environments, but its potential for spatial analysis has been underutilized due to a lack of versatil...

www.biorxiv.org

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Reposted by Jan Philipp Kreysing

Philippe Van der Stappen @phaips.vd.st · May 6

Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!

tomoguide.github.io

Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪

Welcome to TomoGuide

A step-by-step Cryo-ET guide

tomoguide.github.io

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Reposted by Jan Philipp Kreysing

Lorenz Lamm @lorenzlamm.bsky.social · Apr 25

🦠🧠 MemBrain update! 🧠🦠
We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics.
🔗 Preprint: doi.org/10.1101/2024...
🔗 Code: github.com/CellArchLab/...
🧵(1/6) #TeamTomo

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 12

Looking for a tool to measure membrane thicknesses in tomograms (#TeamTomo)? Or curious about thickness differences within and across organelles? Check out my fellow @becklab.bsky.social PhD student @deglushk.bsky.social's excellent preprint:
www.biorxiv.org/content/10.1...

www.biorxiv.org

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 12

Thank you, Michaela!

Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 12

Thanks!

Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 11

Finally, we selected a representative fragment of chromatin, modelled it including histone tails, and performed all-atom MD simulations on it. The simulation showed an overall stable molecular arrangement with H4 tails mediating a stacking interaction.

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 11

Examining the 3D heterochromatin organization, we found a 37 nm edge-to-edge distance between connected nucleosomes and two trinucleosome arrangements: a smaller stacked population and a larger one with longer nucleosome distances, suggesting no strict long-range order for native heterochromatin.

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 11

We then used a physics-based model to predict DNA linkers between the nucleosomes obtained by cryo-ET. This allowed us to visualize kbp-long chromatin fragments from inside human cells.

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 11

Meta-analysis on the nucleosome coordinates revealed dense chromatin patches with local concentrations exceeding 200 mg/mL and showed native chromatin behaves like an intermediate between liquid and gas with some short-range order.

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 11

Thanks to these high-confidence peaks, we obtained the highest-resolved in situ chromatosome structure to date (with no interpolation). With local resolutions of core histones near 6Å, we confirmed the secondary structures reported in numerous in vitro studies. #TeamTomo

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 11

First, we enhanced template matching for nucleosomes by generating interpolated tilts between existing ones to reconstruct higher-contrast tomograms. Check out www.biorxiv.org/content/10.1... for method details. #TeamTomo

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 11

We investigated the molecular architecture of heterochromatin using cryo-ET (#TeamTomo) with enhanced template matching, subtomogram averaging, DNA linker predictions, and MD simulations.

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 11

New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 11

Also, check out @sergiocruzleon.bsky.social's post for a cool video summary about our new heterochromatin preprint.

Sergio Cruz-León @sergiocruzleon.bsky.social · Apr 11

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social

🔗 Preprint here tinyurl.com/3a74uanv

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Jan Philipp Kreysing @jpkreysing.bsky.social · Apr 9

Excited to share our latest work on nuclear pore complex scaffold integrity and its perturbation. Now out in Nature Cell Biology: rdcu.be/eg4i9
Great work by Reiya Taniguchi who just opened his own research group back in Japan! 🥳

Nuclear pores safeguard the integrity of the nuclear envelope

Nature Cell Biology - Taniguchi et al. structurally analyse nuclear pore complex architecture in situ during differentiation, which is associated with mechanical constraints on the nuclear...

rdcu.be

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Reposted by Jan Philipp Kreysing

bioRxivpreprint @biorxivpreprint.bsky.social · Mar 15

Automated Removal of Corrupted Tilts in Cryo-Electron Tomography https://www.biorxiv.org/content/10.1101/2025.03.13.642992v1

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Reposted by Jan Philipp Kreysing

Beck Laboratory @becklab.bsky.social · Jan 17

Hello world!

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Reposted by Jan Philipp Kreysing

Max Planck Institute of Biophysics @mpibp.bsky.social · Jan 17

Fresh out of the press! ✨Check out our new paper on the violent entry of the HIV capsid into the nuclear pore — and how it cracks the gate! 🤯 💥 Incredible work from @becklab.bsky.social and @hummerlab.bsky.social 🤩 More here: www.biophys.mpg.de/2842024/hivcapsid-cracks-the-npc?c=2011019 🔗 #teamTOMO

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Jan Philipp Kreysing @jpkreysing.bsky.social · Jan 17

So happy that my main PhD project on HIV-1 nuclear entry is now out in Cell. I want to especially thank my supervisor Martin @becklab.bsky.social and our amazing collaborators @maziarheidari.bsky.social from @hummerlab.bsky.social, Vojtech Zila from the Kräusslich lab and many others.

Beck Laboratory @becklab.bsky.social · Jan 17

In a great collaboration with @hummerlab.bsky.social and the Kräusslich lab: HIV capsid doesn't break at the NPC; instead, it cracks open the NPC itself! Details in Cell: authors.elsevier.com/sd/article/S... @mpibp.bsky.social @uniheidelberg.bsky.social A thread below:

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bioRxivpreprint @biorxivpreprint.bsky.social · Dec 21

cryoTIGER: Deep-Learning Based Tilt Interpolation Generator for Enhanced Reconstruction in Cryo Electron Tomography https://www.biorxiv.org/content/10.1101/2024.12.17.628939v1

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Jan Philipp Kreysing @jpkreysing.bsky.social · Dec 13

Check out our latest preprint if you want to find out what happens when capsid and NPC interact (spoiler: it doesn't seem to end well for the NPC) #teamtomo
www.biorxiv.org/content/10.1...

Passage of the HIV capsid cracks the nuclear pore

Upon infection, human immunodeficiency virus (HIV-1) releases its cone-shaped capsid into the cytoplasm of infected T-cells and macrophages. As its largest known cargo, the capsid enters the nuclear p...

www.biorxiv.org

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