Really hyped to share our pre-print on mtDNA replication-fission ! @nanigrotjahn.bsky.social (doi: doi.org/10.64898/202...) 🧵with details below ⤵️

ATAD3A structurally links mtDNA replication and mitochondrial fission

Mitochondrial function depends on the maintenance of its genome, and disruptions in copy number and distribution are hallmarks of mitochondrial disorders. Mitochondrial DNA (mtDNA) replication is spat...

doi.org

1) The Herzik lab is excited to announce our newest preprint in collaboration with the Grotjahn lab! We have developed a surfactant cocktail that seeks to overcome one of the more nefarious problems in #cryoEM, Air-water interface (AWI)-induced damage and preferred orientation (PO).

Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...

#teamtomo gets another quantitative cell biology tool! We extend our Surface Morphometrics pipeline to measure membrane thickness. Alongside many biological findings, we show that our 3D measurements closely match in vitro vesicle measurements from 2D EM (collab w/Neal Waxham and Fred Heberle).

Journal of Cell Biology@jcb.org · 7mo ago

Medina, Chang et al. of the @nanigrotjahn.bsky.social lab introduce a new method based on the Surface Morphometrics pipeline to measure global and local thicknesses of organellar #membranes from cellular cryo-electron tomography data. rupress.org/jcb/article/... #CryoET

Online today, the journal version of our ( @nanigrotjahn.bsky.social @attychang.bsky.social @mmedina300kv.bsky.social) manuscript from earlier this year describing membrane thickness measurement in cells with #teamtomo! rupress.org/jcb/article/...

In our new preprint, we show how fibril-dynamics of signaling component TIRAP supports sensitive & fast sensing of endotoxin LPS. Congrats to co-lead @arthurfelker.bsky.social. @piehlerlab.bsky.social @arnemoeller.bsky.social #TLR #cryoEM #blender doi.org/10.64898/202...

What an honor to see @attychang.bsky.social’s work featured in @jcb.org The Year in Cell Biology 2025 collection! Even more special that it coincides with my first #cellbio2025 conference 🙂 s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social #teamtomo #cellbio25

Journal of Cell Biology@jcb.org · 8mo ago

@attychang.bsky.social, @nanigrotjahn.bsky.social et al. show that cytoplasmic #ribosomes on #mitochondria alter the local membrane environment for protein import. rupress.org/jcb/article/... 📕 From The Year In Cell Biology: rupress.org/jcb/collecti... #CellBio2025

Just installed Doppio on our Linux machine. This is awesome work making relion more accessible and easy to run. I haven't tried submitting jobs yet but it is already making our live easier! I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!

Sjors Scheres@sjorsscheres.bsky.social · 9mo ago

At some point, Doppio will replace relion's gui. Already you can do more in Doppio than in relion! 🤩

Prohibitins aren’t hanging out just anywhere in the membrane — they prefer the 💁‍♀️💎✨VIP section💅🪩🥂 Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics. s/o to #teamtomo #cryoET co-authors @hamid13r.bsky.social @attychang.bsky.social @baradlab.com

bioRxiv Cell Biology@biorxiv-cellbio.bsky.social · 9mo ago

Prohibitin complexes associate with unique membrane microdomains in cells https://www.biorxiv.org/content/10.1101/2025.11.14.688579v1

So excited that this work is out and I am so grateful to our team @hamid13r.bsky.social @attychang.bsky.social @baradlab.com @nanigrotjahn.bsky.social

Danielle Grotjahn@nanigrotjahn.bsky.social · 9mo ago

Prohibitins aren’t hanging out just anywhere in the membrane — they prefer the 💁‍♀️💎✨VIP section💅🪩🥂 Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics. s/o to #teamtomo #cryoET co-authors @hamid13r.bsky.social @attychang.bsky.social @baradlab.com

Jan-Hannes Schäfer et al.: CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection #Automation #DataProcessing #CryoEM @umich...#IUCr https://journals.iucr.org/paper?S2053230X25008866

CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection

CryoSift is a CNN-based tool that assesses the quality of 2D class averages. The incorporation of CryoSift into cryoSPARC workflows enables automated particle-stack cleaning.

journals.iucr.org

We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated. mrc.tal.net/vx/appcentre...

-80 freezer at -20

Marjorie James Keenan@unenthusiast.com · 10mo ago

In honour of spooky month, share a 4 word horror story that only someone in your profession would understand. rm -rf ~/

I used this opportunity (and github copilot!) to turn this into my first github repository with README and examples, etc. This was a lot of fun! Hopefully, I didn't completely mess it up! github.com/hamid13r/war...

GitHub - hamid13r/warp_remove_skipped_views: Removing etomo skipped views from Warp xml files to improve the tomogram reconstruction.

Removing etomo skipped views from Warp xml files to improve the tomogram reconstruction. - GitHub - hamid13r/warp_remove_skipped_views: Removing etomo skipped views from Warp xml files to improve ...

github.com

Working on #WarpTools I have the old problem of removing "bad tilts". These are views that I skipped in #etomo to get a better model... I wrote a python code to turn the UseTilt to False in the XML files for those views and improve the tomo reconstruction. #teamtomo github.com/hamid13r/war...

warp_lamella_adapters/remove_bad_views.py at main · hamid13r/warp_lamella_adapters

A short optimized pipeline to get lamella tomography (with pretilt and with some tilts obscured or mistracked) to work well with Warp - hamid13r/warp_lamella_adapters

github.com

The SerialEM Python interface has been a huge driver of innovation at the hardware-software boundary in cryo-EM: suddenly the scientist with some programming chops can readily implement their ideas 🥰 This looks like a fantastic meeting!

Guenter Resch@nexperion.net · 11mo ago

Happy to announce "Technical Innovations Using #SerialEM: A Community Meeting", a new format of hybrid meeting David Mastronarde and I are organizing in April 2026. For more info, a preliminary list of speakers, pre-registration etc. visit www.nexperion.net/semcm2026

We all love colours, especially, when they can be generated automatically! Fantastic talk by Danielle Grotjahn @nanigrotjahn.bsky.social linking method development, structural biology and cell biology! #WEHeraeusSeminar #cryoEM #StructuralBiology #Microscopy @arnemoeller.bsky.social

More great cryo-ET benchmarking work from my colleagues Maarten Tuijtel, Tomáš Majtner, Beata Turoňová, & @becklab.bsky.social: Systematic study of how tilt increment choice affects downstream TM & STA. Preprint has the optimally balanced tilt increment. #TeamTomo www.biorxiv.org/content/10.1...

Optimal tilt-increment for cryo-ET

Cryo-electron tomography (cryo-ET) enables high-resolution, three-dimensional imaging of cellular structures in their native, frozen state. However, image quality is limited by a trade-off between ang...

biorxiv.org

Ran out of github copilot prompts while programming and realized I was already depending on in too much :(

It has been an excellent year to be an Iranian scientist working in US academia. Unfortunately, as an immigrant I would rather not to explain any further.

I LOVE this photo of the Grotjahn Lab. Congrats, Dr. Medina! @mmedina300kv.bsky.social

Danielle Grotjahn@nanigrotjahn.bsky.social · last yr.

higher res group pic 🤩

It’s been a big week for the Grotjahn Lab—our very first graduate student, @mmedina300kv.bsky.social, successfully defended her PhD thesis! 🎉 So proud of everything she’s accomplished and grateful for the light she’s brought to our lab from day one ☀️⚡

Apply to our @PhDposition - deadline this Sunday!

Lars-Anders Carlson@lacarlson.bsky.social · last yr.

Repost appreciated: Open #PhDposition in structural virology in my group! Join us in Umeå, 🇸🇪 to uncover how arboviruses remodel the cellular interior. In situ #cryoET combined with #virology, #cellbiology, and #biophysics. Deadline 4 May. More info: www.carlsonlab.se/join/

🚨New preprint!🚨 #teamtomo We expanded Surface Morphometrics to quantify membrane thickness from cryo-ET—revealing local variation across organelles. Led by the lab’s first grad student, @mmedina300kv.bsky.social (defending Monday! 🍾) w/ @attychang.bsky.social @hamid13r.bsky.social & @tomo.science

bioRxivpreprint@biorxivpreprint.bsky.social · last yr.

Surface morphometrics reveals local membrane thickness variation in organellar subcompartments https://www.biorxiv.org/content/10.1101/2025.04.30.651574v1

Our badass graduate student @attychang.bsky.social 's paper is on JCB's cover 🥳🥳🥳

Journal of Cell Biology@jcb.org · last yr.

Our April issue is here! rupress.org/jcb/issue/22... The cover shows a segmented model of cytoplasmic #ribosomes associated with mitochondrial membrane in a Saccharomyces cerevisiae cell. From Ya-Ting Chang, @nanigrotjahn.bsky.social and colleagues (doi.org/10.1083/jcb....)

Repost appreciated: Open #PhDposition in structural virology in my group! Join us in Umeå, 🇸🇪 to uncover how arboviruses remodel the cellular interior. In situ #cryoET combined with #virology, #cellbiology, and #biophysics. Deadline 4 May. More info: www.carlsonlab.se/join/

Imagine this: The same young scientists now trying to get into PhD programs, facing reduced admissions and uncertainty over whether labs can take them on due to NIH funding cuts, also survived high school during peak COVID and navigated college through a pandemic. 😥😒 #standupforscience

I was trying to explain Grotjahn Lab's research to a friend of mine and was struggling to explain the balance of resolution and context. Suddenly, I remembered Atty's paper: Not only we can locate the ribosomes, we can see their orientations, on the surface of the mitochondria outer membrane!

Journal of Cell Biology@jcb.org · last yr.

Ya-Ting Chang, @nanigrotjahn.bsky.social et al. @scripps.edu present a membrane-guided approach for identifying a subset of cytoplasmic #ribosomes oriented for protein import on the surface of #mitochondria in budding yeast using #cryoET: rupress.org/jcb/article/...

For #teamtomo, context is everything. We highlight the power of #surfacemorphometrics in guiding STA and quantitatively assessing the impact of these structures on the local environment. 1st collab paper w/ @zidlab.bsky.social (hopefully many more to come!) @tomo.science @hamid13r.bsky.social

Journal of Cell Biology@jcb.org · last yr.

Ya-Ting Chang, @nanigrotjahn.bsky.social et al. @scripps.edu present a membrane-guided approach for identifying a subset of cytoplasmic #ribosomes oriented for protein import on the surface of #mitochondria in budding yeast using #cryoET: rupress.org/jcb/article/...

Congrats to our postdoc Jan-Hannes Schaefer @jhschaef.bsky.social on being awarded a fellowship from the Walter Benjamin Program! Jan is collaborating with the Kelly lab here at Scripps Research @scripps.edu to understand how transthyretin forms amyloids that lead to heart disease.