sofie.rec

An Asgard archaeon from a modern analog of ancient microbial mats It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon...

Our new preprint with a new #Asgard from stromatolites (and its Desulfobacterota companion). Complete circularised genomes of both, cool #cryoem images, protein modelling, etc

Big group effort with a lot of people involved
#archaeasky #archaea
www.biorxiv.org/content/10.1...

Characterizing organisms from three domains of life with universal primers from throughout the global ocean - Scientific Data Scientific Data - Characterizing organisms from three domains of life with universal primers from throughout the global ocean

Please Re-Post. Our global GRUMP microbial ocean database is out in Scientific Data! Unfractionated, single universal PCR, with Archaea, Bacteria, and Eukaryotes all on the same scale with the same denominator. Pole to pole, depths to 6000m. Lots of metadata. www.nature.com/articles/s41...

After 5 amazing years @pilhoferlab.bsky.social I'm starting my lab @embl.org Grenoble this November embl.org/wollweber
We'll image Asgard archaea and many other strange microbes ( #archaeasky, #protistsonsky..) to understand eukaryogenesis
First job ad: #teamtomo scientist!🔬❄️ tinyurl.com/2rdu2ze6

Excited to share the lab's 1rst preprint! Rapid high-res immunofluorescence is now possible in cultured & environmental diatoms thanks to 4-fold expansion microscopy. A step-change for comparative cell biology in one of the most important phytoplankton groups on the planet 🥳
tinyurl.com/m9s5su7s 1/2

Final PhD paper now reviewed and published in JSB:X. I was happy with some great reviews that improved the paper! Thanks to Sander Roet for his help with the code base, and Remco Veltkamp and @fridof.bsky.social

Are you a recent dinoflagellate convert, or already long dedicated to the craft? Don't you wish you could talk about them more?

Join Manon's DinoSphere seminar series! All things phylogeny, imaging, ultrastructure and more :)

#protistsonsky

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...

Anti-gatekeeping workflows is what keeps #teamtomo growing! Love to see it.

Ribofun!

Check out 'the website' by Phil&Flo - a tomo processing pipeline/tutorial from frame to structure. For easy implementation of the Aretomo3 to RELION5 pipeline, or your students first dataset, get processing!

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 🔬🧪

🦠🧠 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

Join us in Hamburg!

May 6: Advancing Correlative Light & cryo-EM: Bridging Molecular Precision & Tissue Architecture

Register: indico.desy.de/event/48246/

May 9: Beyond the Barrier: Advanced Microscopy of Pathogens in High-Biosafety-Containment Labs

Register: indico.desy.de/event/48139/...

Tissue-like multicellular development triggered by mechanical compression in archaea The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal mul...

#weekendreading🔬📑

Tissue-like multicellular development triggered by mechanical compression in archaea

@science.org #microsky

www.science.org/doi/10.1126/...

Very Happy to finally see this story out.
I remember the first time @archaeon-alex.bsky.social showed me the videos maybe 3-4y ago on a Zoom call !
Mind blown then and still mind blown today.
A must read for all.

The cell’s powerhouses: Molecular machines enable efficient energy production Mitochondria are the powerhouses in our cells, producing the energy for all vital processes. Using cryo-electron tomography, researchers at th...

#Mitochondria power our cells, but how? Using cryo-electron tomography, @cellarchlab.com and @florentwaltz.bsky.social report in @science.org that energy-producing proteins form supercomplexes, optimizing ATP production.

I'm super happy that our story is now published!
📖 www.science.org/doi/10.1126/...
But what changed compared to the original preprint?

Also, I feel i should post Movie 1 🎥, that inspired the cover. Back when I did the original bluesky thread, movies were not available.

Cryo-ET Analysis Unveils the Minimum Structural Unit and Hierarchical Ultrastructure of Silk Fibers in Silkworm and Spider www.biorxiv.org/content/10.1101/2025.03.12.642793v1 #cryoEM

From cytoplasm to lumen-mapping the free pools of protein subunits of three photosynthetic complexes using quantitative mass spectrometry pubmed.ncbi.nlm.nih.gov/40077900/

Activism and Science: Anne Urai and Clare Kelly on responding to the climate and biodiversity crises How an economic framework may inspire new ways to tackle the climate crisis.

1/ Why are so many scientists silent on the climate crisis?

We interviewed neuroscientists @anne-urai.bsky.social & @clarekelly.bsky.social on their participatory workshops designed to stimulate scientists from awareness to activism.
buff.ly/SSf99Q2

Rare cellular events observed in the cryo-ET dataset. Slices through tomograms (left) with corresponding 3D segmentation (middle and right). Right panels show enlarged views of the boxed regions in the middle panels. A) Mitochondrion at the plasma membrane, tethered to microtubules by thin filaments of unknown identity. Segmented classes: nuclear envelope (light blue), nuclear pore complex (dark blue), 80S ribosomes (orange), mitochondrial membranes (dark red), ATP synthase (royal blue), plasma membranes (grey), microtubules (pink), filaments (yellow), endoplasmic reticulum (purple). Zoomed-in panel shows thin filaments running between microtubules and the mitochondrion at the plasma membrane. Note that this tomogram contains two closely appressed cells, and thus, two plasma membranes with cell walls between. B) Mitochondrial fission event with ER membrane interactions. Segmented classes: mitochondrial membranes (dark red), ATP synthase (royal blue), 80S ribosomes (orange), thylakoid membranes (green), PSII (bright yellow), cell wall (grey), ER (purple), fission site containing filamentous structures perpendicular to the mitochondrial long axis (pale yellow). C) Ciliary transition zone between basal body and axoneme, including assembling IFT train and stellate structure77. Segmented classes: microtubule doublets (light blue), central microtubule pair (light green), stellate structure (pale red), IFT train (yellow). D) Pyrenoid tubule extending from the thylakoids into the phase-separated Rubisco matrix of the pyrenoid. Minitubules originate from thylakoid membranes82. Segmented classes: thylakoid membranes (dark green), PSII (yellow), pyrenoid tubule (lime green), Rubisco (lavender blue), minitubules (orange). Scale bars in A-D: 100 nm. Related to Fig. 2C-H.

To all #TeamTomo #CryoET and #Chlamydomonas aficionados: we have updated EMPIAR-11830 with a bug fix concerning some cryo-CARE denoised tomos as well as additional files and metadata! 🎉👩🏽‍💻

www.ebi.ac.uk/empiar/EMPIA...

A little thread about what's new... 🧵 1/n

We (@cellarchlab.com peeps, @manondemulder.bsky.social @phaips.vd.st @fannyleblanc.bsky.social @computingcaitie.bsky.social and Ricardo) had a blast at the EMBO in situ meeting in Heidelberg! Meeting old friends and making new ones! Lots of cool science and new ideas to try 👨🏻‍🔬🔬

Have you used #network_analyses in the past to analyse your #ecology data? Have you wondered how many of those correlations actually represent interactions between #microorganisms? Here I present a paper how we leveraged #protistsonsky to evaluate the validity of the method. A thread:

Raman microscopy of cryofixed biological specimens for high-resolution and high-sensitivity chemical imaging Cryofixation and low-temperature Raman observation allows the accumulation of Raman signals for highly sensitive chemical imaging.

Raman microscopy of cryofixed biological specimens for high-resolution and high-sensitivity chemical imaging | Science Advances www.science.org/doi/10.1126/...

Ok everything's going to shit, but I just screenprinted plankton in blacklight ink a la fluorescence microscopy and I'm super into it! Tried a phase contrast image too- it sorta worked. If you have any fluorescent images you'd like me to do feel free to reach out. #sciart #copepod #diatom

Screenprinting fluorescence microscopy images in blacklight ink, part II. Still need to hone the technique, but I'm looking for more images so feel free to reach out if you have any to share. Could make a nice blacklight LED frame for ya too. Cultured cell image by Derek Sung. #sciart #biology

Wait till they view it with expansion microscopy.

Excited to share our ✨preprint✨ from my work in Ted Wensel's lab! We present novel insights into the photoreceptor-specific roles of CEP290. 🧵👇 Thanks for the helpful participation from everyone involved, especially @mrobichaux.bsky.social and @agostolab.bsky.social! www.biorxiv.org/content/10.1...

What started as a visit to learn ExM by @fburki.bsky.social turned into a full blown ExM workshop, many friends & colleagues, > 25 different species, obviously challenges and some good chat around drinks.

Lets see the #UExM efficieny by End of this Week.

#ProtistsOnSky

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

Microscopy Nodes is now up on bioRxiv! 🚀

This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).

High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬

www.biorxiv.org/content/10.1...