Tomas Pascoa

Check out our new preprint on an integrated pipeline combining in situ #cryo-ET with MALDI #MSImaging for single-cell identification and classification from previously analysed EM-grids.
Link: www.biorxiv.org/content/10.1...

Amyloid reconstructions from cryoSPARC

Helical Reconstruction of Amyloids in cryoSPARC?
We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social.
Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...

Streptophyte algae go #TeamTomo with @thanahartmann.bsky.social!

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/🧵

We have a preprint of a book chapter for you: Structural Analysis of Membrane Proteins in Cell-Derived Microvesicles.

We describe how to image membrane proteins in mid-sized vesicles using cryo-electron tomography

zenodo.org/records/1717...

These results are truly impressive! But I do worry that #cryoEM is moving into a phase where progress is made by optimizing parameter settings for black box programs. The devil is often in the details, and I am not sure how this could be implemented in #relion, as stated, without more info.

Sub-cellular chemical mapping in bacteria using correlated cryogenic electron and mass spectrometry imaging

Congrats Hannah Ochner and authors on this important paper! Strong collaboration with @kiranrpatil.bsky.social

www.biorxiv.org/cgi/content/...
@mrclmb.bsky.social @wellcometrust.bsky.social

Leopard-EM: An extensible 2DTM package to accelerate in situ structural biology The ability to generate high-resolution views of cells with cryogenic electron microscopy (cryo-EM) can reveal the molecular mechanisms of biological processes in their native cellular context. The re...

First pre-print from the Lucas Lab led by Matthew Giammar and @joshdcryoem.bsky.social online today! We develop a new, extensible Python implementation of 2DTM and apply it to build pixel size optimization, constrained search and characterize molecular motions in situ www.biorxiv.org/content/10.1...

If you are thinking about the future of structural biology, we are too! Our two cents (Jürgen Plitzko and I) just got published online here: authors.elsevier.com/sd/article/S...

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...

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...

🚨 Imagine a bacterium that refuses to follow the textbook:
It grows as tangled filaments, divides unevenly, reshapes its own membranes… and even builds grappling hooks.
Meet Litorilinea aerophila — and here’s why it blew our minds.

New preprint: In situ Architecture of #Plasmodesmata.

Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.

🔗 doi.org/10.1101/2025...

🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM

hot (well, cold) off the press! ❄️

well done @glynnca.bsky.social & @michaelgrange.bsky.social & fabulous co-authors 👏🏼

#teamtomo #cryoET

A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries Cryo-electron tomography (cryo-ET) enables 3D visualization of complex biological environments without the need for purification, thereby preserving t…

Happy to say that my Current Opinion in Structural Biology article came out today. I hope it helps to guide to you in using cryo-ET to make new biological discoveries!

www.sciencedirect.com/science/arti...

CryoET tomogram with the gap junction (green), ribosomes (cyan) and microtubules (pink)

In our latest preprint on bioRxiv, we present the in situ structure of
the human gap junction at 14 Å resolution using cryo-ET.

The structure provides a blueprint for investigating how connexin
regulation shapes intercellular communication in health and disease.

Structural and functional analysis of the Mycobacterium tuberculosis MmpS5L5 efflux pump presages a pathway to increased bedaquiline resistance Bedaquiline, an antitubercular drug that targets ATP-synthase, is a key component of a new oral drug regimen that has revolutionized the treatment of multi drug resistant tuberculosis. Clinical bedaqu...

Bedaquiline resistance driven by the MmpS5L5 efflux pump is threatening the drug regimens used to treat MDR-TB.

In our new preprint, we used structural and genetic approaches to better understand how MmpS5L5 effluxes bedaquiline and how future resistance may evolve. 🧵🔽

#TBsky #MicroSky #TB

Interactions between TTYH2 and APOE facilitate endosomal lipid transfer - Nature The Tweety homologue TTYH2 is identified as the lipid transfer mediator for APOE-containing lipoproteins.

Interesting new structure of the Tweety protein TTYH2 complexes with delipidated ApoE
www.nature.com/articles/s41...

Delighted to see our work in press! 🙌🔬🧠

Thanks to @glynnca.bsky.social, @michaelgrange.bsky.social and the rest of the fabulous co-authors for all your contributions.

Excited to see where in tissue structural cell biology goes next 👀!

#liftlaughlove #teamtomo #whopper

Proud to share our latest paper. doi.org/10.1016/j.cr...

Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue.

Structural biology in tissue is well and truly here!

@rosfrankinst.bsky.social

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

Proud to present the lab's latest work. The full structure of the sodium translocating methyltransferase (Mtr) bound to a small oxygen-responsive small protein MtrI. Work by Tristan and together with @schmitzstreitslab.bsky.social .

www.biorxiv.org/content/10.1101/2025.06.02.657420v1

We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.

Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.

cryotud.github.io/locscale/

Happy to present the lab latest work, today from the green-side. The ultimate PSII assembly intermediate that directly precedes incorporation of the Mn4O5Ca cluster and formation of the OEC. Psb32 binds to PsbV, challenging the assumption the extrinsic subunits all associate spontaneously in-vivo.

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 🔬🧪

My (also imperfect) solution is to use MobaXterm. The built-in X server works to display napari (launched on the HPC) on the local machine. I find it obviously slower than running napari locally, but good enough for this sort of application - and very easy to set up

Are you into cryo-ET, in-cell discovery, protein translocation and folding or just cool integration of structural biology, proteomics and bioinformatics? Then see our new work:

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

Thank you to all coauthors for your amazing work!

Figure 4. MemBrain v2 end-to-end workflow detects periodic phycobilisome organization. A: Raw tomogram slice of EMD-31244. B: Out-of-the-box MemBrain-seg segmentation (light blue). C: A single membrane instance can be visualized in Surforama and manually annotated with GT phycobilisome positions (magenta). D: MemBrain-pick localizes particles (trained with data from C) on all membranes in the tomogram. E: MemBrain-stats computes Ripley’s O statistic using the positions from D with a bin size of 5nm. The distance between peaks (35 nm) was measured to estimate chain unit spacings.

We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples!

Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵

#CryoET #TeamTomo
www.biorxiv.org/content/10.1...

Come do cool science with us!

And what a way to start!!!!

Fantastic work! Congrats to @fidelormz.bsky.social @sophia-pa.bsky.social @rnfr2d2.bsky.social @schullerjm.bsky.social and everyone else involved!