What if you could cut out sub cellular structures and measure the proteome? SPEx: Compartment-Resolved Proteomics via Expansion MicroscopyβGuided Microdissection
www.biorxiv.org/content/10.6...
awesome work by Curdin Franziscus, @imcf-lex.bsky.social,
@biehli.bsky.social, Alexander Schmidt!
Transient molecular chimerism for exploiting xenogeneic organelles www.nature.com/articles/s41... @natcomms.nature.com
Partitioning of Rubisco activase into the pyrenoidal Rubisco condensate is mediated by a functional protein-protein interaction www.nature.com/articles/s41... @natcomms.nature.com
#TeamTomo if you want to use CTF-corrected 3D subtomos from AreTomo3 in RELION v.5.1 you can use this updated script:
github.com/Phaips/aretomo3torelion5
I'm excited to share *Stoic*, a method for fast and accurate protein complex stoichiometry prediction directly from sequence. Preprint: www.biorxiv.org/content/10.6... π§΅π(1/10)
Stoic: Fast and accurate protein stoichiometry prediction (preprint header with authors and affiliations)
Meet Stoic from @daniil-litvinov.bsky.social and @ninjani.bsky.social: embeddings to predict stoichiometry of protein complexes from sequence fast and accurately π§¬π§©π»π€©
www.biorxiv.org/content/10.6...
Interesting! Will definitely give this one a go. Thanks!
Absolutely! We see often that STOPGAP performs much better for initial alignments especially for hard(er) targets with low particle number
Thanks for the inputs! Maxsig I use mostly for memory reasons (without any noteable difference in outcome) and when using the E-limit I arrive at the same result even when set well above (binned) Nyquist
Confirmed by gold-standard FSC of course :)
pytom-match-pick does not use projections unlike RELION5 and I suppose there is also quite the difference from the previous pseudo-subtomos
What I saw is even with priors the local alignment can diverge. More rigorous restriction then enabled from being stuck at ~12 Γ to going all the way to ~5 Γ (sub 4 Γ locally)
New OpenFold3 preview out! (OF3p2)
It closes the gap to AlphaFold3 for most modalities.
Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratchπ§΅1/9
Yes! :) Thanks for raising this, it is an important aspect. I usually start around 20-30Γ and the maps reach ~5Γ with AF3 model agreement and features not present in the template.
To be more clear this is what I meant with the angular distributions:
left without and right with sigma_ang 3 using 3.7 degrees local searches for both
Template matching gives us good priors and in my hands if given exhaustive sampling the angular distributions fall into a small set of values (local minima?) whereas when restricting to local angular searches of 3 stddev they stay in broad distribution
started using --π¬π’π π¦π_ππ§π π in RELION5 Refine3D and all of a sudden every subtomogram average goes to high resolution π€―
#TeamTomo
Excited to announce Iβm starting a new lab at @gmivienna.bsky.social (Vienna BioCentre) in Sept 2026
We study how carbon fixation is inherited and maintained in algae using cryo-ET, imaging, environmental sampling&more
Looking for people who want to build the lab together, get in touch!
#teamtomo
Amazing work congrats everyone! π₯³
Our work on #hornwort #pyrenoids is finally out in @science.org! π We uncovered how hornworts pack their Rubisco into pyrenoids and successfully recreated them in Arabidopsis. A key step toward engineering more efficient photosynthesis in crops @btiscience.bsky.social www.science.org/doi/10.1126/...
A cartoon from the 1950βs thatβs more relevant than ever π
Happy Birthday #AFM!
To celebrate the first description of the atomic force microscope (AFM) in Physical Review Letters, we spoke to our longstanding honorary member Christoph Gerber, who, together with Carl Quate and Gerd Binnig, invented this groundbreaking instrument.
@unibas.ch bit.ly/4raqCOm
The Summer Call for our prestigious, fully funded #PhDFellowships is now open to talented early-career scientists worldwide.
π¬ Rotation-based program
π International community
π Apply by May 8, 2026
Apply now and join a leading life sciences institute!
www.biozentrum.unibas.ch/phd/internat...
Itβs FREE to publish in Journal of Cell Science β there are no page charges, colour charges or hidden fees. And if your institution has a Read & Publish agreement, you can publish immediate OA free of charge.
Find out more: journals.biologists.com/jcs/pages/re...
#forscientists
#notforprofit
ChimeraX screenshot showing CubeNTube plugin.
The new ChimeraX CubeNTube plugin allows erasing parts of maps using cube, cylinder, and custom shapes and has undo. Created by Tamino Cairoli. Available from ChimeraX menu Tools / More Tools....
The best stories are the personal ones. So before we get to the new preprint, stay awhile and listen
#MobileLabs #TREC
@embl.org at its best: collaborative, open, transformative, and just the right amount of crazy. Dreaming of mechanistic cell biology *in the natural environment*? Dream no more, rent the AML.
www.biorxiv.org/content/10.6...
www.youtube.com/watch?v=jepb...
#WeFreezeOnTheBeach #ProtistsOnSky π¦ ππ§ͺ
Introducing AlphaFast π. AF3 is transformative but too slow for large-scale protein design. My students Ben and Jeonghyeon made it 10-100x faster using GPU-accelerated sequence search.
Preprint: www.biorxiv.org/content/10.6...Β
Code: github.com/RomeroLab/al...
π Weβre hiring! The Structural Biology Platform is seeking a Project Leader to advance cryo-electron tomography and expand capabilities at the FMI. Join a vibrant research community at the interface of structural biology, cell biology & disease mechanisms. Apply at: www.fmi.ch/education-ca...