Marcel Dickmanns | 🌿❄️🔬
@madic.bsky.social
Shooting electrons, ions and photons (mainly) at plants to study cell-cell communication @mpibiochem.bsky.social & @hhu.de
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..
You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.
This saves some clicking around. Neat!
This saves some clicking around. Neat!
October 7, 2025 at 2:54 PM
You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.
This saves some clicking around. Neat!
This saves some clicking around. Neat!
Haha yes! Some more contenders in rod outer segments, paracrystalline arrays in mitos and ER, funky OSER forms. But hard to argue with stacks of pancakes sustaining global oxygen and food supply🥞🏆
September 27, 2025 at 6:17 PM
Haha yes! Some more contenders in rod outer segments, paracrystalline arrays in mitos and ER, funky OSER forms. But hard to argue with stacks of pancakes sustaining global oxygen and food supply🥞🏆
Remember those tethers, seen to extent from assembly surfaces to PM in tomograms? Their length and positioning matches linker IDRs. C2 domains are known to bind PM lipids within PD. We infer that tethers are MCTP IDRs extending towards the PM, where C2A domains anchor them.
🧵11/n
🧵11/n
July 26, 2025 at 3:38 PM
Remember those tethers, seen to extent from assembly surfaces to PM in tomograms? Their length and positioning matches linker IDRs. C2 domains are known to bind PM lipids within PD. We infer that tethers are MCTP IDRs extending towards the PM, where C2A domains anchor them.
🧵11/n
🧵11/n
You may have noticed the C2A and C2A-B linker domains are not resolved in the average. The reason we found in the linker sequence. They are intrinsically disordered regions (IDRs): glycine-rich, polyampholytic and predicted to be highly prone to phase-separate.
🧵10/n #LLPS
🧵10/n #LLPS
July 26, 2025 at 3:38 PM
You may have noticed the C2A and C2A-B linker domains are not resolved in the average. The reason we found in the linker sequence. They are intrinsically disordered regions (IDRs): glycine-rich, polyampholytic and predicted to be highly prone to phase-separate.
🧵10/n #LLPS
🧵10/n #LLPS
MCTPs integrate into the ER-derived desmotubule membrane and tubulate it via reticulon homology domains (RHDs). They also contact each other via C2 domains; possibly what’s giving stability to the assemblies.
🧵9/n
🧵9/n
July 26, 2025 at 3:38 PM
MCTPs integrate into the ER-derived desmotubule membrane and tubulate it via reticulon homology domains (RHDs). They also contact each other via C2 domains; possibly what’s giving stability to the assemblies.
🧵9/n
🧵9/n
By proteomics, structure prediction and some serious 3D puzzling, we identified the building blocks of the assemblies resolved here: Dimeric MCTP proteins!
🧵8/n
🧵8/n
July 26, 2025 at 3:38 PM
By proteomics, structure prediction and some serious 3D puzzling, we identified the building blocks of the assemblies resolved here: Dimeric MCTP proteins!
🧵8/n
🧵8/n
Subtomogram averaging revealed helical protein assemblies, which are modular and present in all imaged PD across tissues and callose states - core architectural features of PD.
So, what are these things?
🧵6/n
So, what are these things?
🧵6/n
July 26, 2025 at 3:38 PM
Subtomogram averaging revealed helical protein assemblies, which are modular and present in all imaged PD across tissues and callose states - core architectural features of PD.
So, what are these things?
🧵6/n
So, what are these things?
🧵6/n
These wider PD also revealed more of the busy interior: Periodic densities coat the central, ER-derived desmotubule at entrances & tethers connect it to the PM. Central segments lack such coatings.
🧵5/n
🧵5/n
July 26, 2025 at 3:38 PM
These wider PD also revealed more of the busy interior: Periodic densities coat the central, ER-derived desmotubule at entrances & tethers connect it to the PM. Central segments lack such coatings.
🧵5/n
🧵5/n
PD permeability is dynamically regulated. Under stress, e.g. pathogen infection or temperature shifts, plants deposit #callose at the cell wall, narrowing PD apertures, reducing permeability. We induced callose deposition (*) and found it can fully sever ER, PM and cytosolic continuity.
🧵3/n
🧵3/n
July 26, 2025 at 3:38 PM
PD permeability is dynamically regulated. Under stress, e.g. pathogen infection or temperature shifts, plants deposit #callose at the cell wall, narrowing PD apertures, reducing permeability. We induced callose deposition (*) and found it can fully sever ER, PM and cytosolic continuity.
🧵3/n
🧵3/n
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
Workflows are also applicable to thicker tissues. Examples of #Arabidopsis embryo and epidermal salt glands of the halophyte Limonium bicolor are included. 🧵4/5
February 19, 2025 at 6:06 AM
Workflows are also applicable to thicker tissues. Examples of #Arabidopsis embryo and epidermal salt glands of the halophyte Limonium bicolor are included. 🧵4/5
Subtomogram averaging and spatial analysis of #Rubisco in #Physcomitrium as proof of principle. 🧵3/5
February 19, 2025 at 6:06 AM
Subtomogram averaging and spatial analysis of #Rubisco in #Physcomitrium as proof of principle. 🧵3/5
We use autofluorescence for label-free targeting within high-pressure frozen samples, followed by serial LO. 🧵2/5
February 19, 2025 at 6:06 AM
We use autofluorescence for label-free targeting within high-pressure frozen samples, followed by serial LO. 🧵2/5
Our methods paper made it to bioRxiv:
doi.org/10.1101/2025...
Full #cryoET workflows for #plant tissues. Plus some general tricks and tweaks on serial Lift-Out and cryo-FLM. 🧪🧵1/5
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM #CLEM
doi.org/10.1101/2025...
Full #cryoET workflows for #plant tissues. Plus some general tricks and tweaks on serial Lift-Out and cryo-FLM. 🧪🧵1/5
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM #CLEM
February 19, 2025 at 6:06 AM
Our methods paper made it to bioRxiv:
doi.org/10.1101/2025...
Full #cryoET workflows for #plant tissues. Plus some general tricks and tweaks on serial Lift-Out and cryo-FLM. 🧪🧵1/5
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM #CLEM
doi.org/10.1101/2025...
Full #cryoET workflows for #plant tissues. Plus some general tricks and tweaks on serial Lift-Out and cryo-FLM. 🧪🧵1/5
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM #CLEM
Thanks for the link. Their lumenal reporter protein (LRP) is 2-4nm with pI=4.3.
January 24, 2025 at 3:27 PM
Thanks for the link. Their lumenal reporter protein (LRP) is 2-4nm with pI=4.3.
Thanks! I do like his laser analogy. Though, the pop-out effect of capitalized forms in a wall of text may help readability.
January 22, 2025 at 6:46 PM
Thanks! I do like his laser analogy. Though, the pop-out effect of capitalized forms in a wall of text may help readability.
That's some wild figure labeling for an equally wild new species.
phytokeys.pensoft.net/article/1209...
#PlantScience
phytokeys.pensoft.net/article/1209...
#PlantScience
January 8, 2025 at 12:15 PM
That's some wild figure labeling for an equally wild new species.
phytokeys.pensoft.net/article/1209...
#PlantScience
phytokeys.pensoft.net/article/1209...
#PlantScience
That needle was pretty metal
November 12, 2024 at 1:20 PM
That needle was pretty metal
November 12, 2024 at 12:54 PM
Experiments canceled. On the bright side:
Got to play some more with ChimeraX VR. Could be usefull for model building, but interface and controls are horrible in 3D.
Any recommendations for decent #VR keyboards or voice-to-consol software?
EMDB-7957, PDB-6DLU
🧬🧶
Got to play some more with ChimeraX VR. Could be usefull for model building, but interface and controls are horrible in 3D.
Any recommendations for decent #VR keyboards or voice-to-consol software?
EMDB-7957, PDB-6DLU
🧬🧶
November 1, 2024 at 5:42 PM
Experiments canceled. On the bright side:
Got to play some more with ChimeraX VR. Could be usefull for model building, but interface and controls are horrible in 3D.
Any recommendations for decent #VR keyboards or voice-to-consol software?
EMDB-7957, PDB-6DLU
🧬🧶
Got to play some more with ChimeraX VR. Could be usefull for model building, but interface and controls are horrible in 3D.
Any recommendations for decent #VR keyboards or voice-to-consol software?
EMDB-7957, PDB-6DLU
🧬🧶