Sign in

Philippe Van der Stappen

@phaips.vd.st
352 followers 404 following 36 posts

Cryo-ET of Rubisco phase separation PhD @ Engel & Hondele Lab Biozentrum Basel 𝗖𝗛 #TeamTomo

PostsRepliesMedia
Reposted by Philippe Van der Stappen
Rasmus Jensen @rasmusjensen.bsky.social · 25/09/2026
🎉 Out today in Cell: the paper I've been looking forward to sharing for a long time 🎉 We used cryo-ET to find a molecular machine nobody knew existed on the surface of a minimal bacterium, and worked out what it does. 🧵(1/7) #TeamTomo #cryoET
1023190
Reposted by Philippe Van der Stappen
Florent Waltz @florentwaltz.bsky.social · 22/09/2026
Great success for the 2nd edition of the Young Swiss Tomo Meeting in Bern 🔬, co-organized with the DCI, and @leonieanton.bsky.social, Elsa Bauda, @zanettakechagia.bsky.social and Agnes Moe who's joining the team for the next edition. Thanks to @dectris.bsky.social and @thermofishersci.bsky.social ..
Kuppelraum at Bern university. 70 people attending the conferenceThe organizers
Florent Waltz, Leonie Anton, Elda Bauda, Zanetta Kechagia and Agnes MoeThe view from Uni BernThe organizers plus the workshop teachers, Philippe van der Stappen, Sofie van Dorst and Imre Gonda
2305
Reposted by Philippe Van der Stappen
Janani Durairaj (Jay) @ninjani.bsky.social · 16/09/2026
The PhD and Postdoc application links are now live! Come join me at UNIL to work on deep learning for protein structure, interactions & design. pickybinders.org#open-positions
career5.successfactors.eu
Career Opportunities: PhD student position in deep learning for enzyme structure & catalysis (22980)
03928
Reposted by Philippe Van der Stappen
Ricardo D. Righetto @lifeonthewedge.bsky.social · 08/09/2026
A wild publishing ride to get here... but finally! (first bioRxiv: January 5th, 2024 🙃) Amazing work from @lorenzlamm.bsky.social and colleagues 🤗 Special thanks to the community who jumped early on the boat, sharing feedback and training data to make MemBrain v2 a reality 🙏🏽
nature.com
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography - Nature Methods
MemBrain v2 enables streamlined analysis of membranes in cryo-electron tomography by providing user-friendly tools for membrane segmentation, membrane protein localization and spatial analysis, suppor...
17125
Reposted by Philippe Van der Stappen
Torsten Schwede @torstenschwede.bsky.social · 31/08/2026
Can we predict the stoichiometry of proteins in a complex from their sequences - fast and accurately? Congratulations to the #ECCB2026 🧬 proceedings paper award 🎉 @daniil-litvinov.bsky.social @ninjani.bsky.social @cellarchlab.com academic.oup.com/bioinformati...
Proceedings paper “Stoic: fast and accurate protein stoichiometry prediction”
0367
Reposted by Philippe Van der Stappen
bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 26/08/2026
Unsupervised machine-learning identifies latent pyrenoid states linked to mitotic remodeling defects and CO2-dependent growth www.biorxiv.org/content/10.64898/20…
012
Reposted by Philippe Van der Stappen
Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
110446
Reposted by Philippe Van der Stappen
Ryo Yokoyama @yokoyama-ryo.bsky.social · 19/08/2026
Lateral organization of cytochrome b6f in thylakoid membranes controls photosynthetic electron transfer efficiency www.biorxiv.org/content/10.6...
biorxiv.org
Lateral organization of cytochrome b6f in thylakoid membranes controls photosynthetic electron transfer efficiency
Photosynthetic electron transfer relies on the coordinated function and spatial organization of large protein complexes within the thylakoid membrane. The cytochrome b6f complex (b6f) functionally int...
011
Reposted by Philippe Van der Stappen
Cameron Thrash @jcamthrash.bsky.social · 18/08/2026
As a component of aseptic technique, Bunsen burners do not universally decrease deposition of microbe-containing particles journals.asm.org/doi/full/10.... #jcampubs
77126
Reposted by Philippe Van der Stappen
Jamie Blaza @jnb-lab.bsky.social · 10/08/2026
Permanent academic position as a Lecturer in cryo-ET open at York. We are looking for someone to lead a research program making the most of the stunning advances occurring in cryo-ET. It's a research and teaching post but with a focus on research in the early years. jobs.york.ac.uk/vacancy/lect...
jobs.york.ac.uk
Jobs - The University of York
13838
Reposted by Philippe Van der Stappen
Dimitry Tegunov @dtegunov.bsky.social · 07/08/2026
It’s either that, or In Situ Plus, In Situ Pro, In Situ Ultra, and In Situ Max. With Max reserved strictly for when you put an entire frozen human in the TEM (is anyone working on that yet?)
1232
Reposted by Philippe Van der Stappen
Florent Waltz @florentwaltz.bsky.social · 07/08/2026
We've been seeing a lot of "in situ" lately in titles from fancy journals (not pointing any fingers 👀). I’ve delayed posting this, but as more and more come out, I'm afraid "in situ" is becoming an empty buzzword, much like "near-atomic" was for SPA 🔬 1/n #cryo-ET #cryo-EM #cryoET #cryoEM 🧪
85616
Reposted by Philippe Van der Stappen
Magnus Kjærgaard @proteinmagnus.bsky.social · 03/08/2026
Why do intrinsically disordered proteins behave so weirdly during SDS-PAGE? This is the question we aim to answer in our recent paper: onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
Sequence determinants of the hypomobility of intrinsically disordered proteins in <fc>SDS</fc>‐<fc>PAGE</fc>
Proteins with intrinsically disordered regions (IDRs) migrate at a higher apparent molecular weight in sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, complicating their analysis and...
36625
Reposted by Philippe Van der Stappen
Maria Hondele @mariahondele.bsky.social · 03/08/2026
🚀 New preprint 🥳 Fantastic work by our recent PhD graduate Daan ! How are mRNPs remodeled as they exit the nucleus? We identify PAIP1 as a factor that promotes exchange of the nuclear poly(A)-binding protein PABPN1 for cytoplasmic PABPC1, coupling mRNA export to cytoplasmic mRNP maturation.
12512
Reposted by Philippe Van der Stappen
sofie.rec @sofie-dot-rec.bsky.social · 27/07/2026
The artist formerly known as #thatmitoriboguy has now become #thatchlororiboguy Check out some cool tomo from @florentwaltz.bsky.social @phaips.vd.st
23010
Reposted by Philippe Van der Stappen
Florent Waltz @florentwaltz.bsky.social · 27/07/2026
And 2 complementary 📜: 1️⃣ Cyanobacterial & vascular plant chlororibos🌿 (by @michaelwebster.bsky.social, with contrib from @sofie-dot-rec.bsky.social, @cellarchlab.com & I): biorxiv.org/content/10.64898/2026.07.03.736309v1 2️⃣ Marchantia chlororibos 🥬: biorxiv.org/content/10.64898/2026.07.14.738477v2
0122
Reposted by Philippe Van der Stappen
Florent Waltz @florentwaltz.bsky.social · 27/07/2026
This story is now published in @natplants.nature.com ! 🎉🎩 Check out the final article here: nature.com/articles/s41477-026-02361-1 Very similar to the original bioRxiv preprint, with the addition of some cool polysome analysis (in the supplementals)! Thanks and congrats to everyone involved! 🙏
nature.com
Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome - Nature Plants
Using in situ cryo-electron tomography, researchers found a unique ‘arm’ domain on the small subunit of Chlamydomonas chlororibosomes. This discovery suggests that chlororibosome structure is more evo...
29836
Reposted by Philippe Van der Stappen
Ben Long @botbml.bsky.social · 25/07/2026
Regulatory logic of the Chlamydomonas CO2-concentrating mechanism: coupling carbon flux, energy supply, and pyrenoid architecture www.frontiersin.org/journals/pla...
frontiersin.org
Frontiers | Regulatory logic of the Chlamydomonas CO2-concentrating mechanism: coupling carbon flux, energy supply, and pyrenoid architecture
The algal CO2-concentrating mechanism (CCM) elevates CO2 around Rubisco, the CO2-fixing enzyme, through the coordinated action of inorganic carbon (Ci) uptak...
042
Reposted by Philippe Van der Stappen
Ryo Yokoyama @yokoyama-ryo.bsky.social · 23/07/2026
Regulatory logic of the Chlamydomonas CO2-concentrating mechanism: coupling carbon flux, energy supply, and pyrenoid architecture www.frontiersin.org/journals/pla...
frontiersin.org
Frontiers | Regulatory logic of the Chlamydomonas CO2-concentrating mechanism: coupling carbon flux, energy supply, and pyrenoid architecture
The algal CO2-concentrating mechanism (CCM) elevates CO2 around Rubisco, the CO2-fixing enzyme, through the coordinated action of inorganic carbon (Ci) uptak...
021
Reposted by Philippe Van der Stappen
Martin Jonikas @mjonikas.bsky.social · 22/07/2026
Engineering a pyrenoid into crops could boost yields, but testing components in plants takes months. To accelerate engineering, we made Nicotiana benthamiana with hybrid algal Rubisco, enabling the reconstitution of pyrenoid number regulation in a plant! www.biorxiv.org/content/10.6...
1103
Reposted by Philippe Van der Stappen
James Barrett @james-r-barrett.bsky.social · 22/07/2026
Check it out! Deeper insights into the pyrenoid of Chlorella. More evidence Rubisco has convergently evolved as an organising hub, cool membrane architectures and evidence that most of the rest of the CCM is conserved with other green pyrenoids! 💚 Preprint here 🔗: www.biorxiv.org/content/10.6... 🔗
0215
Reposted by Philippe Van der Stappen
Mihris Naduthodi @mihrisn.bsky.social · 22/07/2026
(3/16) What is a pyrenoid? It is a droplet-like compartment inside the chloroplast that packs Rubisco (the enzyme that fixes CO2) together with a CO2 delivery system, raising local CO2 around Rubisco and making carbon fixation faster and more efficient.
162
Reposted by Philippe Van der Stappen
Mihris Naduthodi @mihrisn.bsky.social · 22/07/2026
(1/16) Nearly two-thirds of ocean carbon fixation flows through a diverse organelle: the pyrenoid. Our new paper maps its 3D architecture in the alga Chlorella and identifies new proteins — expanding the toolkit to engineer this CO2-concentrating machine into crops🧵 #Pyrenoid #CCM #Photosynthesis
13418
Reposted by Philippe Van der Stappen
Jonas Blomme @handle.invalid · 17/07/2026
4/4 Our data supports the convergent evolution of a biomolecular condensate. We show that the main pyrenoid assembly protein, SUPA1, has minimal sequence conservation to characterized unicellular algal Rubisco-condensing proteins, binding to a different surface region of Rubisco.
172
Reposted by Philippe Van der Stappen
Jonas Blomme @handle.invalid · 17/07/2026
3/4 We provide a unique insight into Rubisco condensation. We combine multi-discipline approaches to reveal the helical folding of Rubisco Binding Motifs upon binding, combined with steric hindrance that halves the available binding sites from eight to four.
131
Reposted by Philippe Van der Stappen
Jonas Blomme @handle.invalid · 17/07/2026
Excited to share our latest preprint on #PhycologyFriday. We map out the carbon fixation pathway for the first time in a multicellular alga, the green seaweed Ulva, and reveal a unique Rubisco-Linker interaction in the pyrenoid, a chloroplast condensate. Below I summarize some key points. #seaweeds
34520
Reposted by Philippe Van der Stappen
Ryo Yokoyama @yokoyama-ryo.bsky.social · 14/07/2026
First glimpses into the molecular kaleidoscope of pyrenoid diversity www.sciencedirect.com/science/arti...
sciencedirect.com
First glimpses into the molecular kaleidoscope of pyrenoid diversity
A significant proportion of global photosynthetic carbon fixation relies on the pyrenoid, a biomolecular condensate found in the chloroplast of most u…
021
Reposted by Philippe Van der Stappen
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 10/07/2026
AF-CALVADOS is now published doi.org/10.1002/pro.... We combine AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale: — Ensembles of >12000 full-length human proteins — Comparison of IDRs alone and I n context for >1500 TFs @sobuelow.bsky.social @kejohansson.bsky.social
14014
Reposted by Philippe Van der Stappen
Sophia Paul @sophia-pa.bsky.social · 08/07/2026
Excited to share my paper! 🥳 Today in #Nature we reveal an 8 MDa Hdr electron bifurcating super-assembly in class I methanogens that couples the first and last steps of hydrogenotrophic methanogenesis. A lineage-specific adaptation to anaerobic niches. www.nature.com/articles/s41...
36924
Reposted by Philippe Van der Stappen
Magnus Palmblad @magnuspalmblad.bsky.social · 07/07/2026
Tired of AI-generated figures? I asked our talented scientific illustrator Manon Zuurmond to draw some of the instruments and lab equipment we missed in NIH's otherwise fantastic BioArt resource. First batch now available as CC BY. Free for everyone to use in publications: github.com/Center-for-P...
Drawings of various laboratory equipment (liquid chromatography system, mass spectrometers and a centrifuge).
121889
Reposted by Philippe Van der Stappen
Martin Jonikas @mjonikas.bsky.social · 05/07/2026
The algal pyrenoid turbocharges global CO2 fixation. Central to its function are specialized membranes that deliver CO2. We discovered that the protein RBMP2 makes these membranes—and found that the mysterious minitubules appear to enhance CO₂ delivery! www.biorxiv.org/content/10.6...
1319
Reposted by Philippe Van der Stappen
Ben Long @botbml.bsky.social · 03/07/2026
Mature plant chloroplasts form reversible gyroid cubic membranes www.biorxiv.org/content/10.6...
biorxiv.org
Mature plant chloroplasts form reversible gyroid cubic membranes
Across kingdoms, cells fold their membranes into precise shapes closely linked to their functions. In mature land-plant chloroplasts, the photosynthetic membranes have been viewed as strictly lamellar...
021
Reposted by Philippe Van der Stappen
Biozentrum, University of Basel @biozentrum.unibas.ch · 02/07/2026
New Assistant (tenure-track) or Associate Professor position in Climate #Biophysics! Join our international research community to explore fundamental molecular mechanisms underlying climate-relevant biological processes. Apply by 7 Sept 2026! www.biozentrum.unibas.ch/de/open-posi...
biozentrum.unibas.ch
Assistant/Associate Professor in Climate Biophysics
01611
Reposted by Philippe Van der Stappen
Nancy Moran @nancy-moran.bsky.social · 02/07/2026
A step forward in discovering Buchnera's key to the aphid's heart, published today! Thanks to Jerry Maeda and other authors--a great team -- and to the helpful reviewers #SymbioSky doi: doi.org/10.1038/s415...
doi.org
A secreted endosymbiont protein essential for colonizing host cells - Nature
SyeA was present in the Buchnera ancestor, is secreted into the host cytoplasm, is homologous to secreted effectors of bacterial pathogens and is essential for Buchnera transmission.
210541
Reposted by Philippe Van der Stappen
Ryo Yokoyama @yokoyama-ryo.bsky.social · 01/07/2026
A versatile tool for gene editing in the diatom Thalassiosira pseudonana academic.oup.com/plphys/artic... @plantphys.bsky.social
academic.oup.com
A versatile tool for gene editing in the diatom Thalassiosira pseudonana
An integrated genetic toolkit enables systematic molecular investigation of ocean diatoms, microscopic algae that contribute approximately one-fifth of glo
044
Reposted by Philippe Van der Stappen
Marten Chaillet @martenchaillet.bsky.social · 29/06/2026
From v0.2.0 MissAlignment now has an inference mode where you can apply the trained models from one dataset to a new dataset to skip training time. I haven't tested it extensively, so double check if the results look decent 😉 The program calls changed slightly, see here: github.com/warpem/miss-...
github.com
1269
Reposted by Philippe Van der Stappen
Caitie McCafferty @computingcaitie.bsky.social · 22/06/2026
I will be hiring at all levels so if you are interested and want to learn more, please get in touch! 📻 ❄️ 🔬 🦠 🧬 #cilia #cryoet #proteomics #exm #protistsonsky
2219
Reposted by Philippe Van der Stappen
Caitie McCafferty @computingcaitie.bsky.social · 22/06/2026
Happy to finally share that I will be starting my independent group at the @fmiscience.bsky.social in Feb 2027 in a vibrant new environment. We will use integrative in situ structural cell biology methods to investigate ciliary structure and dynamics in several model (and non-model 👀) systems!!
1215431
Reposted by Philippe Van der Stappen
Martin Jonikas @mjonikas.bsky.social · 15/06/2026
Pyrenoid tubules are essential for supercharging CO₂ fixation, but they're hard to resolve by microscopy. So, we physically expanded cells to see where different proteins go (3 examples below). The central tubule region appears specialized for CO₂ delivery! www.biorxiv.org/content/10.6...
1215
Reposted by Philippe Van der Stappen
Wieczorek Lab @mike-wieczorek.bsky.social · 14/06/2026
New preprint! In collaboration with @xujwet.bsky.social, @pedrobeltrao.bsky.social, and Akhmanova and Beekman groups, we determined the structure of the transition zone microtubule doublet in mammalian motile cilia, providing potential insights into the regulation of IFT: tinyurl.com/fssnevuc
tinyurl.com
Structure of the mammalian ciliary transition zone microtubule doublet
The ciliary transition zone gates bidirectional protein trafficking to maintain the specialized ciliary proteome using microtubule doublets as a scaffold. While ciliary axonemal doublets are well-char...
12915
Reposted by Philippe Van der Stappen
Grant Sanderson @3blue1brown.com · 12/06/2026
Here's an excerpt from the most recent video on how Shannon studied the entropy of English, animated by Mitchell Zemil
111510
Reposted by Philippe Van der Stappen
Félix de Carpentier @fdecarpentier.bsky.social · 12/06/2026
We have just published a detailed, simple, and effective protocol for the electroporation of the microalga Chlamydomonas. Check it out! bio-protocol.org/en/bpdetail?...
0103
Reposted by Philippe Van der Stappen
Martin Jonikas @mjonikas.bsky.social · 11/06/2026
The algal pyrenoid fixes ~1/3 of global carbon, relying on a unique membrane-within-condensate architecture. How is this architecture built? We discovered that the protein MITH1 draws membranes into the pyrenoid condensate by promoting wetting! 🌿💧 www.biorxiv.org/content/10.6...
14616
Reposted by Philippe Van der Stappen
cryoEM papers @cryoempapers.bsky.social · 11/06/2026
Low-Energy Polishing Facilitates Breaking the Resolution Barrier of In Situ Cryo-EM www.biorxiv.org/content/10.64898/2026.06.09.731061v1 #cryoEM
095
Reposted by Philippe Van der Stappen
Journal of Experimental Botany @jxbotany.bsky.social · 31/05/2026
🔬 RESEARCH 🔬 CP12 interacts with phosphoribulokinase in Chlamydomonas reinhardtii. CP12 deletion induces reduced RuBP levels, impacts Rubisco partitioning between stroma and pyrenoid-localized fractions and affects acclimation to low levels of CO2 - Gérard et al. #PlantScience 🧪
Graphical abstract: P12 interacts with phosphoribulokinase in Chlamydomonas reinhardtii. CP12 deletion induces reduced RuBP levels, impacts Rubisco partitioning between stroma and pyrenoid-localized fractions and affects acclimation to low levels of CO2.
11311
Reposted by Philippe Van der Stappen
Allegretti Lab @matteoall.bsky.social · 27/05/2026
We're happy to announce our new preprint! 🐸 easymode: general pretrained networks for cellular cryo-ET. Segment ~20 cellular features – ribosomes, microtubules, mitochondria, nuclei & more – with zero model training. 🔗 doi.org/10.64898/202... 🧵👇
116755
Reposted by Philippe Van der Stappen
bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 22/05/2026
Easymode: general pretrained networks for cellular cryo-ET enable flexible approaches to subtomogram averaging www.biorxiv.org/content/10.64898/20…
0179
Reposted by Philippe Van der Stappen
cryoEM papers @cryoempapers.bsky.social · 21/05/2026
In situ molecular architecture of the mammalian sperm nuclear vacuole www.biorxiv.org/content/10.64898/2026.05.18.725999v1 #cryoEM
063
Reposted by Philippe Van der Stappen
Peter Škrinjar @peterskrinjar.bsky.social · 11/05/2026
Now published in NSMB! Paper: doi.org/10.1038/s415... Full PDF: rdcu.be/fhBtI Overview of additions since the preprint👇 (1/5)
doi.org
Evaluating generalization in protein–ligand cofolding methods - Nature Structural & Molecular Biology
This work introduces the Runs N’ Poses dataset for benchmarking deep learning methods on the protein–ligand complex prediction task. It shows that current methods rely on memorization, challenging the...
23915
Reposted by Philippe Van der Stappen
Martin Jonikas @mjonikas.bsky.social · 07/05/2026
Now published @PNASNews! SAGA1 and SAGA2 localize the starch sheath to the pyrenoid in Chlamydomonas reinhardtii www.pnas.org/doi/10.1073/...
pnas.org
SAGA1 and SAGA2 localize the starch sheath to the pyrenoid in Chlamydomonas reinhardtii | PNAS
Most algae enhance their CO2 assimilation by concentrating CO2 within the pyrenoid, a biomolecular condensate of the CO2-fixing enzyme Rubisco. Man...
03013