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This study completes a trilogy of thylakoid papers in @elife.bsky.social, one every 5 years⏳⌛ Part 1 was my first #CryoET paper: elifesciences.org/articles/04889 Part 2 was my first paper with @wojwie.bsky.social: elifesciences.org/articles/53740 Time flies... so let's start working on Part 4? 🤓🧪

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So, PSII arrays seem to be an artifact of isolating thylakoid membranes. And yet… We still wonder if these beautiful (and likely more static) structures play some physiological role during stress or damage. @wojwie.bsky.social & I wrote a mini-review on this: academic.oup.com/plcell/artic... 12/🧵

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We never saw PSII arrays within intact chloroplasts. However, we spotted them in chloroplasts that broke open and exposed their thylakoids to buffer. This is a known in vitro phenomenon called “thylakoid restacking”. Thus, interactions between arrays in two membranes seem to drive restacking!🤐 11/🧵

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There have been many studies on PSII arrays, including #CryoET showing that they can stack thylakoid membranes together. The arrays also form in thylakoids from a variety of species, even diatoms. So it isn’t just a “plant thing”🌿. The catch is—all these studies looked at isolated membranes 🤔 10/🧵

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But there’s a curious loose end to this story. Scientists have been looking at PSII organization in thylakoids for over 50 years (including some really stunning freeze fracture 🔬😍). Sometimes PSII looks randomly oriented, and other times it forms extended 2D crystalline arrays in the membrane 💠 9/🧵

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We also observed that PSII concentration was uniform throughout each granum, irrespective of distance from the margin. Thus, we propose a simple two-domain model of thylakoid organization in green algae and plants. And yes, we speculate about domain #PhaseSeparation. I await your hate mail 📬🤗 8/🧵

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For decades, the idea has persisted that grana margins have a distinct protein composition and provide a zone where PSI & PSII can intermix. However, our "membranograms" revealed strict lateral heterogeneity between PSI & PSII at the margins, just like we previously observed in green algae 🟦🟨 7/🧵

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Contrary to previous models, our native views showed that grana are not perfect cylinders, but have wavy undulating edges 🌊🏄‍♀️. Here we slice through a few grana🥞 from the top– Do you see all the little protein densities in the membranes?🔍 Those are photosynthetic complexes. How to analyze them? 5/🧵

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Our data enabled us to quantify native thylakoid architecture in the grana. Getting precise numbers is important for modeling photosynthetic regulation. Here’s a comparison to similar measurements made by classical TEM. We’d like to apply #CryoET to the dark-to-light💡 transition in the future. 4/🧵

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We made an interesting observation about plastoglobules, lipid-protein storage droplets that share one leaflet with thylakoid membranes. We saw that plastoglobules often sat within little holes in the thylakoids 🟠🕳️, perhaps increasing the area of the contact site, facilitating exchange 🔄 3/🧵

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Unlike in algae and other phototrophs, plant thylakoids form specialized grana stacks🥞 interconnected by single thylakoids called stromal lamellae. The 3D membrane architecture we observed is consistent with the “helical staircase model” proposed from classical TEM (💚🔬 Andrew Staehelin, RIP). 2/🧵

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Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on! #TeamTomo #PlantScience 🧪 🧶🧬 🌾 elifesciences.org/articles/105... 1/🧵

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Ben Engel @cellarchlab.com · 20/09/2025

Thanks William! Regarding the physiological significance of PSII lattices, please see the "How Fluid are Thylakoid membranes" opinion piece that @wojwie.bsky.social and I wrote here: academic.oup.com/plcell/artic...

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Thanks Alister! That Feynman catchphrase is certainly words to live by for #TeamTomo. I actually used to intro my talks with it. But the trick is in the full quote-- these "easy" observations rely on making our microscopes (and tools for analysis) more powerful. Thanks for your help with #MemBrain 🤗

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Ben Engel @cellarchlab.com · 11/09/2025

Yes, very carefully worded. The null hypothesis must come first, and it can't be ruled out (but there are significant challenges to it?). It was these paragraphs about the alternative hypothesis that got my heart aflutter😍. And again, I'm NO expert, but this seems fairly well considered... no? 🍎🍏

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Ben Engel @cellarchlab.com · 09/09/2025

Thanks @dodonova-sveta.bsky.social for visiting us at the @biozentrum.unibas.ch and giving a fascinating talk on the structures and mysteries of archaeal chromatin. The room was packed!🤓 #ArchaeaSky #TeamTomo 🧪🧶🧬 Check out their lab’s new study on asgard hypernucleosomes: bsky.app/profile/dodo...

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Ben Engel @cellarchlab.com · 27/06/2025

Theme 1 of the embo.org ESCRT meeting: Tentacles across scales 🐙 …from simulated asgard archaea to swirly filaments 🌀 Andela Saric, Adai Colom, Qing-Tao Shen, John McCullough 🧶🧬🧪

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Ben Engel @cellarchlab.com · 27/06/2025

The @embo.org ESCRT meeting was packed with membrane remodeling from every branch of the tree of life🌳. Some awesome science 🧪 highlights in the next posts 🧵. But a first impression… the venue!! Wow, Caux castle up a cogwheel train, overlooking Lac Léman! Perfect! 🌄 Thank you @rouxlab.bsky.social 🤗

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Ben Engel @cellarchlab.com · 12/06/2025

Such a joy to host @gaiapigino.bsky.social as the keynote speaker of our annual @biozentrum.unibas.ch @unibas.ch symposium! It’s amazing how far Gaia and her team have pushed the IFT field. Nice exchange with @computingcaitie.bsky.social and the rest of our group. Thanks for visiting! #TeamTomo 🧪🧶🧬🔬

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Ben Engel @cellarchlab.com · 19/05/2025

And from the other direction (not mirrored I hope 🤚✋). Thanks so much for hosting us. So, Basel last week and Paris this week…. where’s dinner next week? (For those with keen eyes: there’s another member of #TeamTomo in this photo. But who?🔎)

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Ben Engel @cellarchlab.com · 06/05/2025

Thanks a lot @arianebriegel.bsky.social for visiting the @biozentrum.unibas.ch and telling us about your amazing #TeamTomo science. The squid 🦑 bacterial symbiosis cryo-lift out is super cool!! 🤩 #FIBtheWorld 🧪🧶🧬🌊

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Ben Engel @cellarchlab.com · 14/04/2025

“No Water, no Life. No Blue, no Green.”💙💚 @floravincent.bsky.social from @embl.org revealing the beauty of diatom symbiotic interactions, which enable these globally important phytoplankton to adapt to environmental stresses and pollutants. Such cool science here at #EMBOclimateResilience 🧪🌊🌍

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Ben Engel @cellarchlab.com · 14/04/2025

So excited to be here at #EMBOclimateResilience, a cool new meeting integrating cell and planetary scales. Inspiring first night keynotes by Jeremy Farrar (chief scientist of @who.int) and Pam Silver. Thanks for organizing, @monicabettencourt.bsky.social! 🧪🌊🌾🌍

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Ben Engel @cellarchlab.com · 03/04/2025

That's a fancy video. I was certainly surprised to see the Very Important Protein in Plants discovered in a tropical jungle🌴😅. It's pure marketing ofc (The Krios: Now in Black), but I do like the messaging about discovering the molecular world all around us-- including plants and cyanobacteria🧪🧶🧬🔬🌾🌊

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Ben Engel @cellarchlab.com · 19/01/2025

Nice question! Actually, yes a 27 kDa protein (GFP) is visible as a distinct dot in tomograms (even with an old K2 detector). See all the dots decorating PolyQ filaments (green arrowheads, Bäuerlein et al.) and VIPP1-coated membrane tubes (panels O-R, Gupta et al.). The "cell buffer" is smaller! 🧪🧶🧬

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Finally, a bit of bonus trivia... I love Chlamy🌱 so much (a little obsessed), that I drew the central image of Figure 3 by hand with a pencil ✏️ Here it is for anyone who likes #SciArt 👨‍🔬👨‍🎨. Happy to provide a higher res version if anyone wants 🖼️ Go #SammyTheChlamy! 🧪🧶🧬🔬🌊🌾🌍

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The teams validated the potential of this dataset through subtomogram averaging of 7 macromolecules. All but one of these structures went to sub-nanometer resolution🔍🔬 Check out this nucleosome by @aliciakmichael.bsky.social and Ricardo. The alpha helices of the histones are clearly resolved! 🧪🧶🧬

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Equally monumental was the job of curating and processing this dataset, led by Ricardo Righetto & @cryosagar.bsky.social, with a lot of support from members of our lab. Great team effort! The Chlamy tomograms contain a diverse selection of organelles, segmented here by @jessheebner.bsky.social 🧪👩‍🔬👩‍🎨

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This large dataset is the result of years of collaborative #TeamTomo work between @abhaykot.bsky.social's TFS team, our @biozentrum.bsky.social group, and the @mpibiochem.bsky.social crew led by John and Jürgen. Abhay's team used automated plasma #FIB milling and 42 overnight #cryoET sessions! 🧪🔬💪

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Ben Engel @cellarchlab.com · 26/12/2024

Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍 Preprint📜: www.biorxiv.org/content/10.1... A short thread🧵👇

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Haha, that’s funny— I’ve been playing the same game this holiday but 10x. Made it today. So now we are real scientists? 😅

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Ben Engel @cellarchlab.com · 18/12/2024

It was fun taking some very serious science pictures with @phaips.vd.st about life in our @biozentrum.bsky.social lab for the @sniunibas.bsky.social INSight issue. Take a look inside for the fancy animated GIFs 🧪🌾🔬 bsky.app/profile/sniu...

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Ben Engel @cellarchlab.com · 17/12/2024

No, I wouldn't smoke in the lab, silly! This is me😉🫧🫧🫧

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Ben Engel @cellarchlab.com · 17/12/2024

Thanks Thibaut! My evolution of asking ChatGPT to preview the look... No that's too sexy, make it ironic. OK, put him in a lab. Did I get it yet? 🤪

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Ben Engel @cellarchlab.com · 17/12/2024

...adding that to my Christmas tenure present list right now🎁 Undecided if I should also go for tweed. Is this the look?😅

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Thanks Jamie!😊 We got a bit unlucky with the timing. Cell has a few special issues to celebrate its 50th anniversary🎂, and we landed in the Neuroscience one. They design their own images for these, so we had no chance. Fair enough... but I'll let others judge the image they used instead👀 #SciArt?

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Thanks to all our amazing collaborators in Japan🇯🇵 (Ginga, Yusuke, Aki, Genji), UK🇬🇧 (Onyou, Sabina, @jnb-lab.bsky.social, Luke) & France🇫🇷 (@serenaflori.bsky.social, Giovanni). And huge congrats to Manon Demulder!👩‍🔬💪 Here's a beautiful #NotTheCover of diatoms on a grid by Martin Oeggerli #SciArt🧪🎨 7/🧵

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Environmental sequencing from Tara Oceans⛵ shows that the PyShell is abundant in oceans around the world! And another mystery: PyShell genes are also found in haptophytes such as E. huxleyi, despite this clade being quite distant from diatoms. What is the evolutionary history of the PyShell?🧪🌍🌊 6/🧵

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So many mysteries remain!🤓 How do sugar metabolites pass through the PyShell, and is it impermeable to CO2 or O2? How does the PyShell bind Rubisco? How is the pyrenoid cut in half during cell division, and how does it again double in size (how to insert new Rubisco and shell subunits)? 🧪🧶🧬🌊🌾 5/🧵

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Our model for how the PyShell enforces pyrenoid architecture to supply Rubisco with a high concentration of #CO2. The CO2-providing membranes are misplaced in the mutants. Comparing to CCMs in cyanobacteria and green algae, we ask whether the PyShell also serves as a diffusion barrier🤔 🧪 🧶🧬🌊🌾 4/🧵

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