Research group at Kavli Institute for Nanoscience. CryoEM methods, membranes, intracellular immunity. By lab members.
Delft en Provence, NL
Joined September 2021
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This was a hard shell to crack: happy to share our preprint on the structure of microbial gas vesicles, giant gas-filled protein shells used by aquatic bacteria and archaea to regulate their buoyancy. biorxiv.org/content/10.1101/…
Maarten and Joel's HRA toolkit is now online at @IUCrJ. Roodmus allows sourcing and waymarking structural ensembles from MD simulations to generate high-quality cryo-EM micrographs for developing/evaluating heterogenous reconstruction algorithms. edu.nl/b7j6t
Work led by Maarten and Joel and a fun collaboration with Tom Burnley @ccp_em and James Parkhurst @RosFrankInst.
Code: github.com/ccpem/roodmus
Datasets: journals.iucr.org/m/issues/2…
Happy to see this out in its final form.
Tanja and Clémence show how intracellular immune effectors form coats on gram-negative membranes to encapsulate cytosol-invasive bacteria:
nature.com/articles/s41594-0…
Thanks @instructhub for help in making conformation-specific nanobodies and @SanderTansLab for OT assays + Cecilia, Natasha, Luca, Stefan and Els .
Also check out complementary work from Oli Daumke's lab looking into the activation mechanism of GBP1 (PMID 38267655).
Very proud of the lab's newest doctor.
Congratulations Dr. @Stefan_T_Huber! 🥳🥳🥳🥳
Fantastic defense, including great questions from @RouslanEfremov & @TassosPerrakis, and another amazing PhD movie from our lab-grown Green Screen Productions. Woot woot!
Jakobi Lab 🇳🇱🇵🇹🇿🇦🇫🇷🇩🇪🇬🇷🇮🇳🇮🇹🇻🇳 retweeted
Only five days remaining ⌛️until the registration deadline for our course 🎓Integrative structural biology: solving molecular puzzles in Hamburg. Apply now! 👉👉👉👉👉embl.org/about/info/course-a…
Quick reminder that the application deadline for our ‘Solving Molecular Puzzles’ course is approaching (25 August).
Apply to join us in November!
Looking to learn all about combining data from different experimental and structure prediction methods to build detailed models of biomolecular complexes?
Apply and join us in Hamburg!
edu.nl/nbakh
Jakobi Lab 🇳🇱🇵🇹🇿🇦🇫🇷🇩🇪🇬🇷🇮🇳🇮🇹🇻🇳 retweeted
Want to learn more about this great collaboration with @CryoTUD...? Joel from the CCP-EM group gave a @ccpbiosim seminar describing benchmarking cryoEM heterogeneous reconstruction methods with Roodmus youtu.be/M83LBW7WCHY
New preprint for birdwatchers 🙂
edu.nl/p7a9x
Maarten & Joel developed Roodmus (= rosefinch), a toolkit that sources MD simulations for benchmarking heterogeneous reconstruction algorithms.
At #ccpem symposium? Visit their poster!
Fun collab w/ @ccp_em & @J2002uk.
We previously showed that a coincident FM-FIB-SEM can be turned into a 4D-STEM system for in situ thickness determination (edu.nl/8xh97).
Daan applied this to cryogenic samples, allowing automated, thickness-controlled milling of frozen-hydrated lamella from cells.
Together with the fluorescence-based targeting capability of the coincident FM, the live thickness estimation by q4STEM and TFI allowed us to perform unsupervised, fluorescence-targeted milling of high-quality lamella with predefined thickness from multiple cells.
Work led by Daan, Radim (who implemented q4STEM with RT specimen) & Clémence (who made all the samples) + Wiel (who juggles our scopes), and another joyful collaboration with the Hoogenboom lab @ImPhys_TUDelft.
Link to preprint: edu.nl/wjka3
All feedback welcome 🙂
Jakobi Lab 🇳🇱🇵🇹🇿🇦🇫🇷🇩🇪🇬🇷🇮🇳🇮🇹🇻🇳 retweeted
Excited to unveil our productive collaboration @lab_baum @RouxLab, featuring 3 co-first authors @diorge_souza, @jespadas91, and @sami_chaaban! Special thanks to @ERR_Moody, Tomo Hatano, and @SPOREMOHAN @tweethinking for their invaluable contributions!
We're thrilled to share our new preprint: "Evolutionarily Conserved Principles of ESCRT-III-Mediated Membrane Remodeling Revealed by a Two-Subunit Asgard Archaeal System."
biorxiv.org/content/10.1101/…
This is the crowd who made it to the finish line of the Dutch Cryo-EM school! 🇳🇱🔬
It was a great privilege and a lot of fun to host the next generation of #teamspa and #teamtomo together with @Ludo_cryoEM & @TzviyaZBM . The future of cryo-EM in NL is bright!
Many thanks to all our tutors & speakers: @WimJHH, @SjorsScheres, @FriedrichForst1, @psirez, @BogdanToader0, @ccp_em, @iadanza_g, @ MaxGemmer, Alok Bharadwaj, Rangana Warshamanage, Agnel Joseph, Joe Greet, Maarten Joosten, Emanuel Katzmann, Oliver Raschdorf 🙏
Day 4 of the Dutch Cryo-EM School with @SjorsScheres and @ccp_em delving into the fundamentals of SPA and treating heterogeneity.
Jakobi Lab 🇳🇱🇵🇹🇿🇦🇫🇷🇩🇪🇬🇷🇮🇳🇮🇹🇻🇳 retweeted
Today we kickoff the Dutch cryo-EM school organjsed by @TzviyaZBM @CryoTUD and @NeCEN_2p0 It will run over the week cover all aspects of TEM, SPA and tomo
Jakobi Lab 🇳🇱🇵🇹🇿🇦🇫🇷🇩🇪🇬🇷🇮🇳🇮🇹🇻🇳 retweeted
I’m thrilled to be able to announce that we were granted a NWO Summit grant entitled ‘Evolving Life from Nonlife’ (EVOLF) with 40 million euro for a 10-year project aimed to cross the gap between non-life and life by assembling a living synthetic cell from lifeless biomolecules!
New preprint for birdwatchers 🙂
edu.nl/p7a9x
Maarten & Joel developed Roodmus (= rosefinch), a toolkit that sources MD simulations for benchmarking heterogeneous reconstruction algorithms.
At #ccpem symposium? Visit their poster!
Fun collab w/ @ccp_em & @J2002uk.