Tomas Pascoa
@tomaspascoa.bsky.social
Postdoc at the Schuller Lab - Synmikro Marburg 🇩🇪
Cryo-EM/ET of anaerobic CO₂ fixation
Cryo-EM/ET of anaerobic CO₂ fixation
Reposted by Tomas Pascoa
Prohibitins aren’t hanging out just anywhere in the membrane — they prefer the 💁♀️💎✨VIP section💅🪩🥂
Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics.
s/o to #teamtomo #cryoET co-authors
@hamid13r.bsky.social
@attychang.bsky.social
@baradlab.com
Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics.
s/o to #teamtomo #cryoET co-authors
@hamid13r.bsky.social
@attychang.bsky.social
@baradlab.com
Prohibitin complexes associate with unique membrane microdomains in cells https://www.biorxiv.org/content/10.1101/2025.11.14.688579v1
November 17, 2025 at 12:22 AM
Prohibitins aren’t hanging out just anywhere in the membrane — they prefer the 💁♀️💎✨VIP section💅🪩🥂
Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics.
s/o to #teamtomo #cryoET co-authors
@hamid13r.bsky.social
@attychang.bsky.social
@baradlab.com
Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics.
s/o to #teamtomo #cryoET co-authors
@hamid13r.bsky.social
@attychang.bsky.social
@baradlab.com
Reposted by Tomas Pascoa
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
Icecream: High-Fidelity Equivariant Cryo-Electron Tomography
Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...
www.biorxiv.org
October 23, 2025 at 11:13 AM
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
Reposted by Tomas Pascoa
Hey #TeamTomo …would you like to try some 🍦ICECREAM!? Our @unibas.ch colleagues over at the @ivandokmanic.bsky.social lab have developed a stunningly effective tool to de-noise and de-wedge your tomograms. The contrast and details will give you brain freeze! 🍨❄️🤯
Please try, we need feedback 🧪🧶🧬🔬
Please try, we need feedback 🧪🧶🧬🔬
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
Icecream: High-Fidelity Equivariant Cryo-Electron Tomography
Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...
www.biorxiv.org
October 23, 2025 at 5:57 PM
Hey #TeamTomo …would you like to try some 🍦ICECREAM!? Our @unibas.ch colleagues over at the @ivandokmanic.bsky.social lab have developed a stunningly effective tool to de-noise and de-wedge your tomograms. The contrast and details will give you brain freeze! 🍨❄️🤯
Please try, we need feedback 🧪🧶🧬🔬
Please try, we need feedback 🧪🧶🧬🔬
Reposted by 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...
Link: www.biorxiv.org/content/10.1...
September 19, 2025 at 6:07 PM
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...
Link: www.biorxiv.org/content/10.1...
Reposted by Tomas Pascoa
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...
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...
October 5, 2025 at 4:16 AM
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...
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!
Gisela Hartmann @thanahartmann.bsky.social from @schullerjm.bsky.social lab in Marburg is telling us more about Cryo-Electron Tomography: Revealing the native cellular organization of streptophyte algae #MAdLand2025
October 2, 2025 at 1:39 PM
Streptophyte algae go #TeamTomo with @thanahartmann.bsky.social!
Reposted by Tomas Pascoa
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/🧵
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
September 25, 2025 at 6:00 PM
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/🧵
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
Reposted by Tomas Pascoa
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...
We describe how to image membrane proteins in mid-sized vesicles using cryo-electron tomography
zenodo.org/records/1717...
Structural Analysis of Membrane Proteins in Cell-Derived Microvesicles
zenodo.org
September 22, 2025 at 12:36 PM
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...
We describe how to image membrane proteins in mid-sized vesicles using cryo-electron tomography
zenodo.org/records/1717...
Reposted by Tomas Pascoa
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.
This one is a bit of a departure from the usual and definitely a work in progress!
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
September 21, 2025 at 7:42 AM
Reposted by Tomas Pascoa
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
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
August 31, 2025 at 6:44 PM
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
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
Reposted by Tomas Pascoa
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...
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...
www.biorxiv.org
August 30, 2025 at 12:49 AM
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...
Reposted by Tomas Pascoa
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...
August 23, 2025 at 11:21 PM
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...
Reposted by Tomas Pascoa
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...
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...
www.biorxiv.org
August 23, 2025 at 9:18 AM
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...
Reposted by Tomas Pascoa
🚨 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.
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.
August 20, 2025 at 10:34 AM
🚨 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.
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.
Reposted by Tomas Pascoa
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
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
July 26, 2025 at 3:38 PM
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
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
Reposted by Tomas Pascoa
hot (well, cold) off the press! ❄️
well done @glynnca.bsky.social & @michaelgrange.bsky.social & fabulous co-authors 👏🏼
#teamtomo #cryoET
well done @glynnca.bsky.social & @michaelgrange.bsky.social & fabulous co-authors 👏🏼
#teamtomo #cryoET
July 21, 2025 at 8:55 PM
hot (well, cold) off the press! ❄️
well done @glynnca.bsky.social & @michaelgrange.bsky.social & fabulous co-authors 👏🏼
#teamtomo #cryoET
well done @glynnca.bsky.social & @michaelgrange.bsky.social & fabulous co-authors 👏🏼
#teamtomo #cryoET
Reposted by Tomas Pascoa
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...
www.sciencedirect.com/science/arti...
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…
www.sciencedirect.com
July 8, 2025 at 9:44 PM
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...
www.sciencedirect.com/science/arti...
Reposted by Tomas Pascoa
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.
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.
July 8, 2025 at 5:33 AM
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.
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.
Reposted by Tomas Pascoa
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
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
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...
www.biorxiv.org
June 26, 2025 at 10:30 AM
Reposted by Tomas Pascoa
Interesting new structure of the Tweety protein TTYH2 complexes with delipidated ApoE
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
June 26, 2025 at 4:02 PM
Interesting new structure of the Tweety protein TTYH2 complexes with delipidated ApoE
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Tomas Pascoa
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
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
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
June 19, 2025 at 9:23 AM
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
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
Reposted by Tomas Pascoa
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
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
June 17, 2025 at 10:59 AM
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
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
Reposted by Tomas Pascoa
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
pytom-match-pick: A tophat-transform constraint for automated classification in template matching pubmed.ncbi.nlm.nih.gov/40475324/ #cryoem
June 9, 2025 at 6:56 AM
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
Reposted by Tomas Pascoa
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
www.biorxiv.org/content/10.1101/2025.06.02.657420v1
June 4, 2025 at 7:10 PM
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
www.biorxiv.org/content/10.1101/2025.06.02.657420v1
Reposted by Tomas Pascoa
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/
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/
May 22, 2025 at 10:10 AM
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/
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/