Marcel Dickmanns | πΏβοΈπ¬
@madic.bsky.social
Shooting electrons, ions and photons (mainly) at plants to study cell-cell communication @mpibiochem.bsky.social & @hhu.de
Pinned
New preprint: In situ Architecture of #Plasmodesmata.
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
π doi.org/10.1101/2025...
π§ͺπ§΅1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
π doi.org/10.1101/2025...
π§ͺπ§΅1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
(couple years later AF2 dropped and 'do we still need to crystallize small domains?' became a valid question)
November 25, 2025 at 6:26 PM
(couple years later AF2 dropped and 'do we still need to crystallize small domains?' became a valid question)
As undergrad I had to purify and crystallize a new protein that kept aggregating no matter what. In distress fantasized about an algorithm to predict good buffer conditions & mutations.
This dataset + whatβs in PDB already would be a decent start.
This dataset + whatβs in PDB already would be a decent start.
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
November 25, 2025 at 6:24 PM
As undergrad I had to purify and crystallize a new protein that kept aggregating no matter what. In distress fantasized about an algorithm to predict good buffer conditions & mutations.
This dataset + whatβs in PDB already would be a decent start.
This dataset + whatβs in PDB already would be a decent start.
Reposted by Marcel Dickmanns | πΏβοΈπ¬
We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the #Arabidopsis #1001GenomesPlus project. We have now a curated collection of over 500 long read genomes.
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Next generation of 1001 Genomes Plus browser and data download
Please indicate all features you would like to see in a browser that displays features of completely sequenced Arabidopsis thaliana genomes
docs.google.com
November 24, 2025 at 2:49 PM
We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the #Arabidopsis #1001GenomesPlus project. We have now a curated collection of over 500 long read genomes.
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Reposted by Marcel Dickmanns | πΏβοΈπ¬
Why IDPs Are Poor Candidates for Homotypic LLPS
π§΅πA thread
π§΅πA thread
November 20, 2025 at 6:32 PM
Why IDPs Are Poor Candidates for Homotypic LLPS
π§΅πA thread
π§΅πA thread
Dewars are full to the rim with green stuff. But someone might..
November 20, 2025 at 11:01 AM
Dewars are full to the rim with green stuff. But someone might..
Bar: 15 um.
November 19, 2025 at 3:45 PM
Bar: 15 um.
Microtubule-based vacuum cleaner π
Cellular structure self-organizes through an interplay between internal mechanisms and external cues. The single-celled suctorian P. collini builds a trap structure to capture large prey using microtubule feeding tentacles, creating feedback between cell morphology and prey availability.
November 19, 2025 at 3:35 PM
Microtubule-based vacuum cleaner π
Reposted by Marcel Dickmanns | πΏβοΈπ¬
Registration is open to take part in the Molecular Biology of Plants (#MBP2026), which especially invites early career scientists to present their molecular #plantsci research www.pflanzen-molekularbiologie.de/en/conferenc...
October 31, 2025 at 2:33 PM
Registration is open to take part in the Molecular Biology of Plants (#MBP2026), which especially invites early career scientists to present their molecular #plantsci research www.pflanzen-molekularbiologie.de/en/conferenc...
Reposted by Marcel Dickmanns | πΏβοΈπ¬
My main work as postdoc @plantophagy.bsky.social lab in @gmivienna.bsky.social is out in @natplants.nature.com π±π
We asked how can protein complexes diversify without compromising their function and explored this question using the plant #exocyst complex.
www.nature.com/articles/s41...
We asked how can protein complexes diversify without compromising their function and explored this question using the plant #exocyst complex.
www.nature.com/articles/s41...
Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape - Nature Plants
The evolutionary diversification of an exocyst subunit was enabled by electrostatic shifts leading to its dissociation from the ancestral complex.
www.nature.com
October 31, 2025 at 1:57 PM
My main work as postdoc @plantophagy.bsky.social lab in @gmivienna.bsky.social is out in @natplants.nature.com π±π
We asked how can protein complexes diversify without compromising their function and explored this question using the plant #exocyst complex.
www.nature.com/articles/s41...
We asked how can protein complexes diversify without compromising their function and explored this question using the plant #exocyst complex.
www.nature.com/articles/s41...
Reposted by Marcel Dickmanns | πΏβοΈπ¬
New OA Article: "In situ architecture of the nuclear pore complex of the higher plant Arabidopsis thaliana" rdcu.be/eNFiR
Advanced imaging techniques and computer modelling to create a detailed structural model of a nuclear pore complex from a seed plant.
Advanced imaging techniques and computer modelling to create a detailed structural model of a nuclear pore complex from a seed plant.
October 31, 2025 at 12:55 PM
New OA Article: "In situ architecture of the nuclear pore complex of the higher plant Arabidopsis thaliana" rdcu.be/eNFiR
Advanced imaging techniques and computer modelling to create a detailed structural model of a nuclear pore complex from a seed plant.
Advanced imaging techniques and computer modelling to create a detailed structural model of a nuclear pore complex from a seed plant.
and striped shirts
October 26, 2025 at 12:05 PM
and striped shirts
The argument is that "under review" is fine, but "under review at X" should not be a quality proxy. Also, if preprinted, you get a doi to put on the CV and ppl can actually read your work regardless of crazy review times.
October 25, 2025 at 8:49 PM
The argument is that "under review" is fine, but "under review at X" should not be a quality proxy. Also, if preprinted, you get a doi to put on the CV and ppl can actually read your work regardless of crazy review times.
Curious which parameters everyone uses to consider res pairs as potentially interacting. Thoughts?
My set for screening (AND):
Side chain heavy atom distance <= 4.2 Γ
PAE <= 8 Γ
Combined pLDDT >= 140
pDockQ > 0.3
My set for screening (AND):
Side chain heavy atom distance <= 4.2 Γ
PAE <= 8 Γ
Combined pLDDT >= 140
pDockQ > 0.3
I love AlphaFoldβbut please include PAE (Predicted Aligned Error) plots for every βinteraction.β Pretty PDBs β proof. If the PAE doesnβt show an interface, it ainβt one. Show the plots. Structural biology's reputation is on the line.
October 25, 2025 at 10:17 AM
Curious which parameters everyone uses to consider res pairs as potentially interacting. Thoughts?
My set for screening (AND):
Side chain heavy atom distance <= 4.2 Γ
PAE <= 8 Γ
Combined pLDDT >= 140
pDockQ > 0.3
My set for screening (AND):
Side chain heavy atom distance <= 4.2 Γ
PAE <= 8 Γ
Combined pLDDT >= 140
pDockQ > 0.3
+bird poo
October 24, 2025 at 8:56 PM
+bird poo
Reposted by Marcel Dickmanns | πΏβοΈπ¬
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 Icecreamπ§
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 Icecreamπ§
Reposted by Marcel Dickmanns | πΏβοΈπ¬
@delaconcepcionjc.bsky.social from @gmivienna.bsky.social (a @johninnescentre.bsky.social alumnus) delivered his 2026 Early Career Research Award Lecture on NLR engineering and his ongoing cryo-ET work! #BiochemEvent
October 22, 2025 at 9:21 AM
@delaconcepcionjc.bsky.social from @gmivienna.bsky.social (a @johninnescentre.bsky.social alumnus) delivered his 2026 Early Career Research Award Lecture on NLR engineering and his ongoing cryo-ET work! #BiochemEvent
Reposted by Marcel Dickmanns | πΏβοΈπ¬
Second, Iβm slowly getting to be in the camp that proteins donβt have functions but instead have properties. What biology does with those properties is a somewhat different matter. So maybe we need to predict properties (kcat, Kd, etc) as well
October 15, 2025 at 2:58 PM
Second, Iβm slowly getting to be in the camp that proteins donβt have functions but instead have properties. What biology does with those properties is a somewhat different matter. So maybe we need to predict properties (kcat, Kd, etc) as well
Great read & perspective!
"We can't leave all the fun to the biologists; we should zoom out while they zoom in."
"We can't leave all the fun to the biologists; we should zoom out while they zoom in."
I wrote a blog post about the future of structural bioinformatics.
Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?
Let me know what you think.
jgreener64.github.io/posts/struct...
Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?
Let me know what you think.
jgreener64.github.io/posts/struct...
Where next for structural bioinformatics?
jgreener64.github.io
October 17, 2025 at 5:19 AM
Great read & perspective!
"We can't leave all the fun to the biologists; we should zoom out while they zoom in."
"We can't leave all the fun to the biologists; we should zoom out while they zoom in."
Reposted by Marcel Dickmanns | πΏβοΈπ¬
Very happy and proud to share the #Spirogyra genome: 50 Mbp small, lacking almost all plastid division proteins and many transcription factors. Kudos to all the many people involved in this multi year project!
@jandevries.bsky.social
@watertoland.bsky.social
www.biorxiv.org/content/10.1...
@jandevries.bsky.social
@watertoland.bsky.social
www.biorxiv.org/content/10.1...
October 11, 2025 at 9:20 AM
Very happy and proud to share the #Spirogyra genome: 50 Mbp small, lacking almost all plastid division proteins and many transcription factors. Kudos to all the many people involved in this multi year project!
@jandevries.bsky.social
@watertoland.bsky.social
www.biorxiv.org/content/10.1...
@jandevries.bsky.social
@watertoland.bsky.social
www.biorxiv.org/content/10.1...
Lovely irony with the typo in the last one.
October 9, 2025 at 1:02 PM
Lovely irony with the typo in the last one.
Reposted by Marcel Dickmanns | πΏβοΈπ¬
β¨Excited that the main project of my PhD is now available as a pre-print on #bioRxiv
Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo
π www.biorxiv.org/content/10.1...
Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo
π www.biorxiv.org/content/10.1...
October 8, 2025 at 3:59 PM
β¨Excited that the main project of my PhD is now available as a pre-print on #bioRxiv
Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo
π www.biorxiv.org/content/10.1...
Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo
π www.biorxiv.org/content/10.1...
Reposted by Marcel Dickmanns | πΏβοΈπ¬
New blog post. In which I analyze the new HHMI announcement and what it means for the science publishing ecosystem openrxiv.org/preprint-man...
Preprint mandates gather momentum - openRxiv
By Richard Sever, PhD. Chief Science & Strategy Officer, openRxiv Preprints speed up science by enabling researchers to disseminate reports of new findings immediately. They also represent a simple wa...
openrxiv.org
October 6, 2025 at 6:53 PM
New blog post. In which I analyze the new HHMI announcement and what it means for the science publishing ecosystem openrxiv.org/preprint-man...
No didn't look yet. Was thinking to pull one by one via uniprot ID (sequence and MSA), but agree a full db would be nice.
October 7, 2025 at 8:48 PM
No didn't look yet. Was thinking to pull one by one via uniprot ID (sequence and MSA), but agree a full db would be nice.
Could pull MSAs from the DB now and save couple hours of CPU time.
October 7, 2025 at 3:15 PM
Could pull MSAs from the DB now and save couple hours of CPU time.