SF does Easter right, between that and hunky jesus

The deadline to register for the 2026 Cryo-ET Workshop has been extended extended to April 10! Learn more about this hands-on workshop and apply at: myumi.ch/lsi-cryo-workshop-2026
@jbquerido.bsky.social @shyamalm.bsky.social

Surprised not to see Arnold ruled out? Has there been an update on her?

And maybe some TARDIS for filaments!

I am getting excited about teaching at this! I think we're going to do copick, membrain-seg, morphometrics, and surforama on my day!

GitHub - GrotjahnLab/surface_morphometrics at configurable-thickness-workflow Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging. - GitHub - GrotjahnLab/surface_morphometrics at configurable-thickness-workflow

If you are feeling brave, feel free to try github.com/GrotjahnLab/...

Note: the example data doesn't have tomograms (and the tomograms we originally used don't have resolved bilayers) so you'll need to supply your own data (or empiar/data portal data).

Right now, the config file is not used in the thickness scripts - you edit the scripts themselves instead. I have working thickness config in a branch pending more extensive testing - the primary challenge is ensuring the tomogram and segmentation get matched up properly.

thickness_plots.py, not singular

Membrane thickness is in the thickness_scan.py and thickness_plot.py scripts right now, which aren't fully incorporated into the standard config setup, but will be very soon as part of the larger rewrite.

GitHub - GrotjahnLab/surface_morphometrics: Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging. Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging. - GrotjahnLab/surface_morphometrics

I've been working on Surface Morphometrics for a new version (coming soon), and made some significant (AI-assisted) performance improvements, especially in pycurv (20-50x!). If you've had technical issues or just felt like it was too slow, give it another try! #teamtomo github.com/GrotjahnLab/...

This was such a fun collaboration - and the new measurement tools kicked off some cool new directions for our lab!

We are running the cryo-ET image processing workshop again this year! Come learn everything tomo: STA, segmentation, heterogeneity analysis from @baradlab.com @williamnwan.bsky.social and others!

Apply!

We resolved the molecular architecture of a condensate—inside cells. 🤯 By combining in situ cryoET with multiscale simulations, we show how a single point mutation modifies molecular interactions, shifts the condensate’s material properties, and alters its biological function. Preprint 👇

I'd bet this one gets a full in-depth discussion later this quarter!

We'll do another one of these in a month or so, and in the mean time will do a few in depth discussions of single papers - will share those as they come! The landscape of #teamtomo papers is increasingly cool and diverse, and its amazing to see both the quantity and quality of recent work.

And finally, my nomination: Beautiful imaging of lrrk2 microtubule decoration changes under different inhibitor conditions showing diverging phenotypes between different inhibitors, from the Leschziner and Villa labs. www.biorxiv.org/content/10.6...

Second to last, from the Schnupf lab, some imaging of the super weird/cool attachment machinery in commensal segmented filamentous bacteria: www.nature.com/articles/s41....

“Kiss-shrink-run” unifies mechanisms for synaptic vesicle exocytosis and hyperfast recycling Synaptic vesicle (SV) exocytosis underpins neuronal communication, yet its nanoscale dynamics remain poorly understood owing to limitations in visualizing rapid events in situ. Here, we used optogenet...

Back to biology with an instant classic: Time-resolved capture of synaptic vesicle exocytosis through "Kiss, Shrink, Run" from Pak Ming Lau, Hong Zhou, and Guo-Qiang Bi www.science.org/doi/10.1126/....

3D-printable bio-sourced nanocomposite hydrogels based on two polysaccharide components: hydroxypropyl guar macromolecules and cellulose nanocrystals Hydrogels are soft and wet materials which require enhanced mechanical properties and toughness. For this aim, double-network hydrogels were prepared …

In a cool change of pace to the world of biomaterials, some tomographic analysis to quantify organization of composite hydrogels. www.sciencedirect.com/science/arti...

Incredible work from the Mizuno lab capturing the process of axon regeneration. On-grid axotomies!! www.nature.com/articles/s41...

Imaging of specialized plant cell walls by improved cryo-CLEM and cryo-electron tomography Cryo-focused ion beam scanning electron microscopy (cryo-FIBSEM) has become essential for preparing electron-transparent lamellae from cryo-plunged and high-pressure frozen specimens. However, targeting specific cellular features within large, complex organs remains challenging. Here we present a series of technical improvements significantly enhancing the efficiency and accessibility of the Serial Lift-Out and SOLIST (Serialized On-grid Lift-In Sectioning for Tomography) procedures that are revolutionizing the field. We were able to extend the cryo-FIBSEM session from 24 hours to 5 days without interruptions. In addition, we describe a modified silver-plated EasyLiftTM needle that eliminates the need of the copper or gold block between the original tungsten needle and the sample. Moreover, we describe a strategy that significantly reduces curtaining effects. Finally, we report a precise routine to target a lamella with a precision of approximately 1 µm in X,Y and Z. Together, these modifications considerably reduce contamination risk and preparation time, making cryo-lift-out techniques more accessible for routine structural biology applications on any type of tissue. Here, we demonstrate the power of our technique by targeting several specific wall structures that are of crucial importance for root function in plants and that were previously inaccessible to cryo-electron tomography (cryo-ET). High-pressure freezing (HPF) of plant tissues presents unique challenges for cryo-electron microscopy sample preparation due to the overall sample size, the individual cells size, their rigid cell wall and finally, their large vacuoles, which contain large amounts of rather diluted water solutions compared to cytosol. The internal root structures targeted are the Casparian strip (CS), suberin lamellae (SL), as well as secondary wall of xylem vessels, requiring reaching a targeting precision of 5 μm in a 3 mm long and 80-120 μm thick root tip. Our technological improvements for the cryo-correlative light and electron microscopy (cryo-CLEM) workflow enabled successful, targeted cryo-ET in plant roots. We noticed that, despite ice formation in vacuoles and to some degree in the cytosol, the plasma membranes and cell walls are remarkably well preserved, providing stunning insights into the native, hydrated nano-structure of plant cell walls, previously only observable with contrasting agents and in a dehydrated state. ### Competing Interest Statement The authors have declared no competing interest.

Some really nice recent work from the Geldner and Genoud groups advancing tissue-scale tomography tools to study plant cell wall organization: www.biorxiv.org/content/10.1.... Maybe we need to start silver-coating our grids at OHSU?

Two people highlighted a recently updated preprint doing cryoEM and cryoET on Flotillin complex structure and organization from Qiang Guo and Ning Gao labs. www.biorxiv.org/content/10.1.... Related work from the MacKinnon lab: www.pnas.org/doi/10.1073/...

Fourth: Incredible imaging and analysis of luminal microtubule associated proteins in neurons from the Mahamid and Baumeister labs. www.pnas.org/doi/10.1073/...

Third: Imaging of intestinal microvilli in c elegans larvae and mice shows some beautiful protein structure decoration, from Xueming Li's and Guangshuo Ou's labs. www.pnas.org/doi/10.1073/... From 2022, practically an old classic!

The In Situ Structure and Distribution of V-ATPase in C. elegans Apical Membrane Stacks The cuticle of Caenorhabditis elegans is an apical extracellular matrix composed primarily of collagens which protects the organism from external stresses and facilitates mobility. The cuticle directl...

Next: In situ structure and localization of V-atpase in a cool c elegans organelles (from Simone Mattei's lab). Nice analysis of a challenging serial liftout sample and a ribosome-guided tomogram refinement approach. www.biorxiv.org/content/10.6...

Structural reorganization underlying stress-induced cytoplasmic solidification in yeast Cells employ diverse strategies to rapidly adapt to sudden environmental changes. In yeast, cytoprotective solidification in response to starvation and energy depletion (ED) has been reported and asso...

First up: Yeast stress-induced remodeling from the Mahamid group: www.biorxiv.org/content/10.6.... Tons of cool visualization of protein oligomerization across two yeast species!

Happy new year #teamtomo! We've resumed our OHSU tomo journal club, and this year I am going to be sharing it on bluesky. This week we did a roundtable, where attendees each brought a paper and did a 3-5 minute discussion of what they thought was cool about it. Here are the papers they discussed!

Hopefully the message is - we should be thinking quantitatively about the organization of our cells and how it correlates to the protein structures we look at within the cell using #teamtomo!

Prohibitin complexes associate with unique membrane microdomains in cells Prohibitins are multi-subunit protein complexes implicated in a variety of roles in mitochondria, including maintaining cristae architecture, regulating lipid metabolism, and mediating protein quality...

More recently, we've also discovered a protein (prohibitin) that seems to either prefer or generate thinner membranes no matter where it is found within the inner mitochondrial membrane: www.biorxiv.org/content/10.1...

Cryo-electron tomography reveals coupled flavivirus replication, budding and maturation Flaviviruses replicate their genomes in replication organelles (ROs) formed as bud-like invaginations on the endoplasmic reticulum (ER) membrane, which also functions as the site for virion assembly. ...

This is a method that built out of a really cool collaboration with @lacarlson.bsky.social right around when I was moving to my independent lab - the journal version of that paper is also almost here! In that work, we show that TBEV replication organelles are thicker than the ER they bud off of.