Ben Engel
banner
cellarchlab.com
Ben Engel
@cellarchlab.com
cellarchlab.com Univ. of Basel Biozentrum🇨🇭. Exploring molecular architecture inside cells with #CryoEM #TeamTomo. Plants and algae in a changing climate. ❄🔬 OF 🌿 4THE 🌍!
Pinned
The #ChlamyDataset is on the cover of @cp-molcell.bsky.social 🖼️🥰!

Read @lifeonthewedge.bsky.social's great thread🧵 for the inside scoop🍨 on all the #TeamTomo developments already made possible since these 1829 tomos hit EMPIAR 🧪 🧶🧬

For more, here's the old preprint thread:
bsky.app/profile/cell...
This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!

This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍

[Maybe long thread ahead]
Reposted by Ben Engel
For #ECR’s:

DBG’s Hot Tpoic Workshop
on Cryo-Electron Tomography + FIB-milling

13 – 15 April 2026
In @cellarchlab.com 's lab @biozentrum.unibas.ch

Organised by @tamb-o.bsky.social, Karen Zinzius, @fannyleblanc.bsky.social

Details: www.deutsche-botanische-gesellschaft.de/en/about-us/...
Hot Topic Conference
Support for an "Eduard Strasburger Hot Topic Conference" for DBG's members
www.deutsche-botanische-gesellschaft.de
February 3, 2026 at 5:24 PM
Reposted by Ben Engel
Our new paper, out today! We resurrected ancient nitrogenases first used by life on Earth 3 billion years ago. We combined synthetic biology and geology & validated their chemical #biosignature in rocks that helps reveal ancient life on Earth!(and beyond!)

Link: www.nature.com/articles/s41...
Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years - Nature Communications
The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient microbes shaped Earth’s nitrogen cycle and offering a new experimental ...
www.nature.com
January 30, 2026 at 9:12 PM
Reposted by Ben Engel
Check this new study on carbon concentration mechanisms!

See how the pyrenoid changes by modifying Rubisco linkers in our favorite alga, Chlamy 💚!

My desk mate @phaips.vd.st spent a lot of time collecting & carefully analyzing these beautiful tomograms 🔬.

Congrats to all the authors!
How does molecular valency shape condensate assembly and function? We used the CO2-fixing organelle in algae—the pyrenoid—to find out… 🧵

Preprint here!:
www.biorxiv.org/content/10.6...

@cellarchlab.com @phaips.vd.st @biologyatyork.bsky.social
#Rubisco #PhaseSeparation #Condensates #Pyrenoid
January 30, 2026 at 7:40 PM
That is a really beautiful poster!🤩 🧪

Inside the Pyrenoid: How Multivalency Shapes Rubisco Organization and CO2 Fixation
www.biorxiv.org/content/10.6...
Lastly, if you prefer to see this as a poster, you can find that here:
james-r-barrett.github.io/presentation...
January 30, 2026 at 4:27 PM
Reposted by Ben Engel
You like #LLPS? #TeamTomo? #Rubisco? Check out our latest preprint!

What a great collaboration this has been!
How does molecular valency shape condensate assembly and function? We used the CO2-fixing organelle in algae—the pyrenoid—to find out… 🧵

Preprint here!:
www.biorxiv.org/content/10.6...

@cellarchlab.com @phaips.vd.st @biologyatyork.bsky.social
#Rubisco #PhaseSeparation #Condensates #Pyrenoid
January 30, 2026 at 3:38 PM
Reposted by Ben Engel
Check out this cool thread on the latest preprint by Gaurav Kumar, @james-r-barrett.bsky.social, @phaips.vd.st from our lab and colleagues, dissecting the physics of Rubisco condensates!

You're in for some stunning #cryoET of the pyrenoid - in Chlamy, of course 😉

Congrats to all involved!
How does molecular valency shape condensate assembly and function? We used the CO2-fixing organelle in algae—the pyrenoid—to find out… 🧵

Preprint here!:
www.biorxiv.org/content/10.6...

@cellarchlab.com @phaips.vd.st @biologyatyork.bsky.social
#Rubisco #PhaseSeparation #Condensates #Pyrenoid
January 30, 2026 at 3:54 PM
Excited to share this detailed biophysical study of #PhaseSeparation in the Pyrenoid, an algal microcompartment that fixes a third of the Earth's #CO2 🌏. We combine methods across scales, in vitro 🧪 and in vivo 🦠

Thanks for the very fun collaboration! 🤗
#PlantScience 🌾 #TeamTomo 🔬 #LivingPhysics 🧬🧶
How does molecular valency shape condensate assembly and function? We used the CO2-fixing organelle in algae—the pyrenoid—to find out… 🧵

Preprint here!:
www.biorxiv.org/content/10.6...

@cellarchlab.com @phaips.vd.st @biologyatyork.bsky.social
#Rubisco #PhaseSeparation #Condensates #Pyrenoid
January 30, 2026 at 3:50 PM
Reposted by Ben Engel
How do diatom cells maintain a constant supply of carbon for photosynthesis? Our microelectrode measurements of the phycosphere around individual diatom cells show that diatoms can rapidly switch between distinct carbon acquisition pathways. @thembauk.bsky.social www.science.org/doi/10.1126/...
January 14, 2026 at 9:49 AM
#TeamTomo visualizes amazing (green 💚♻️) proteasome crystals in yeast. This project was a long time coming -- I remember talking to Cordula about it back when I was a postdoc in Martinsried. Some really cool and surprising findings here. Nice to see it out, and congrats to all the authors! 🧪 🔬
January 30, 2026 at 10:34 AM
SHAPES being the key word, amirite @nanigrotjahn.bsky.social
github.com/GrotjahnLab/...

Should be an interesting #TeamTomo talk. Check it out! 🧪 🔬
WEBINAR: Dr. Danielle Grotjahn, Scripps Research discusses how #cryoET shapes our understanding of cellular architecture, and analyzing data to extract quantitative insights: 10 Feb, 5 PM CET | 11 Feb, 5 AM CET

Register here: ter.li/zfiv48

#CellBiology #StructuralBiology #ElectronMicroscopy
January 23, 2026 at 12:45 PM
Go #TeamTomo! 🧪 @wilflinglab.bsky.social & @nanigrotjahn.bsky.social are on a roll! Beautiful in-cell visualization of lysosome rupture 🎈💥
LLOMe has long been used to study lysosomal damage, yet how it works has remained a mystery.
Using cryo-electron tomography, we show it forms amyloid structures inside lysosomes that mechanically rupture membranes – revealing a new paradigm for lysosomal failure.

🔗 doi.org/10.64898/202...

#CryoET
January 20, 2026 at 8:36 PM
One of the best #TeamTomo studies of phase-separated condensates I’ve seen. I am reminded of Rubisco condensates (pyrenoids) for the ability to make such quantitative measurements of molecular organization. It really helps to have intrinsic ~500 kDa fiducials. Awesome mechanistic stuff!! 🧪 🧶🧬 🔬
We are excited to share our new preprint which is now available to read on biorXiv: doi.org/10.64898/202... 🎉🎉🎉
January 18, 2026 at 8:45 PM
This large-scale open dataset and the continued community development around it exemplify the spirit of #TeamTomo 🧪 🔬 👨‍🔬👩‍💻
Excited to see this work on the cover of #MolecularCell. A massive, open #cryoEM #cryoET dataset capturing molecular organization inside intact cells, pushing what’s possible for #visualproteomics, method development, and computational reuse. Congratulations to the authors.
ter.li/of4cgh
January 18, 2026 at 8:40 AM
This large-scale open dataset and the continued community development around it exemplify the spirit of #TeamTomo 🧪 🔬 👨‍🔬👩‍💻
Congratulations to the team and their work that made the cover of Molecular Cell. A massive, open #cryoET dataset that captures molecular organization inside intact cells and pushes what’s possible for visual proteomics, method development, and computational reuse. 👉 ter.li/of4cgh
January 18, 2026 at 8:40 AM
Reposted by Ben Engel
I'm so happy to have gotten the opportunity to work on this project and I'm SO excited that they selected our image for the cover!
This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!

This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍

[Maybe long thread ahead]
January 9, 2026 at 7:20 PM
Reposted by Ben Engel
What a great example of collaborative science enabled by people sharing things early on. Well done @lifeonthewedge.bsky.social and others!
This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!

This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍

[Maybe long thread ahead]
January 9, 2026 at 9:28 PM
The #ChlamyDataset is on the cover of @cp-molcell.bsky.social 🖼️🥰!

Read @lifeonthewedge.bsky.social's great thread🧵 for the inside scoop🍨 on all the #TeamTomo developments already made possible since these 1829 tomos hit EMPIAR 🧪 🧶🧬

For more, here's the old preprint thread:
bsky.app/profile/cell...
This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!

This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍

[Maybe long thread ahead]
January 9, 2026 at 7:49 PM
Reposted by Ben Engel
#teamtomo gets another quantitative cell biology tool!

We extend our Surface Morphometrics pipeline to measure membrane thickness.

Alongside many biological findings, we show that our 3D measurements closely match in vitro vesicle measurements from 2D EM (collab w/Neal Waxham and Fred Heberle).
Medina, Chang et al. of the @nanigrotjahn.bsky.social lab introduce a new method based on the Surface Morphometrics pipeline to measure global and local thicknesses of organellar #membranes from cellular cryo-electron tomography data. rupress.org/jcb/article/...

#CryoET
January 6, 2026 at 1:51 AM
ER-associated single-capped vaults are surprising and really cool!🤩 Some even contain ribosomes. Vault function is still mysterious but a role in protein quality control seems plausible.

Also great to see Dicty in the #TeamTomo spotlight! #ProtistsOnSky @kgeissler.bsky.social @becklab.bsky.social 🧪
December 28, 2025 at 12:54 PM
Reposted by Ben Engel
Another #notTHECover unfortunately.

But this gorgeous, Tron-like vibe, drawn by the amazing @munafomarzia.bsky.social for our recent #ExM work with @gautamdey.bsky.social & @centriolelab.bsky.social will still be printed out in the lab.

Read here: www.cell.com/cell/fulltex...
December 26, 2025 at 11:53 AM
December 28, 2025 at 4:37 AM
Reposted by Ben Engel
Really excellent work by the bluesky-less Marie and Sara +coauthors in our lab @embl.org! Check it out for cool combinations of light microscopy and #cryoET, and if you're interested in how yeasts reorganize structurally in response to stressors. #teamtomo
December 25, 2025 at 6:10 PM
Reposted by Ben Engel
A super detailed protocol + video on Cryo-ExM - Cryo-Expansion Microscopy, led by the labs of our former postdocs @marinelap.bsky.social & @ebertiaux.bsky.social.
Clear, practical, and very useful for anyone doing nanoscale imaging 🚀 app.jove.com/t/68595/expa...
December 25, 2025 at 1:41 PM
Reposted by Ben Engel
Final version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social

Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.

Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET
December 19, 2025 at 4:45 PM
Reposted by Ben Engel
Happy to see IsoNet2 performing so well on the #ChlamyDataset EMPIAR-11830. Congrats to the authors really great work.
However, I have to say this tomogram looks amazing because the lamella is way too thin (~50 nm) and not vitreous! 🫠

www.biorxiv.org/content/10.6...
December 12, 2025 at 5:18 PM