Ben Barad

Very excited to announce that my first, first author paper, is now on BioRxiv! In this paper we unambiguously show #COPII coated vesicles in unperturbed human cells for the very first time!!

Make my day and check it out!
www.biorxiv.org/content/10.1...

#Cryo-ET #TeamTomo #Cryo-CLEM ❄️🔬❄️🔬❄️🔬❄️🔬

Very cool that it works this way!

This is obviously outrageous, but also thank you for the service you did before it got ripped away!

I'm at the OHSU PREP research symposium and I am so impressed with our trainees, they present and know their project background better then many a graduate student. All the more I'm filled with rage about the cancellation of this wonderful #NIH program 🤬

Wild but also somehow fair that the Thorns don't move up after a pretty clean win against the former #1 ranked team. So much uncertainty still.

Anti-gatekeeping workflows is what keeps #teamtomo growing! Love to see it.

Beautiful work and such a cool mechanism!

A result that was so cool we had to see more how things looked the rest of the time!

They are actually still attached to the ER with continuous membrane (and a macromolecular assembly that keeps them budded) which makes it even crazier - presumably there is still lipid exchange.

Its easy to imagine there being some repetitive artifact in time series data but not quite THAT identical!

So far, no organelle we've seen comes close to the replication organelles from langatvirus infections: www.biorxiv.org/content/10.1...

More than beta testing, the flavivirus story is what got us into this in general! Not to mention the existing work of Fred Heberle, Ilya Levental, and Neal Waxham that inspired the actual density scanning and fitting approach we use.

Local workstation is our (imperfect) solution...

Hard launch for the Park lab at Scripps too for the tomo!

I know print journals aren't exactly on everyone's radar these days, but we’re still geeking out that our latest study—led by the brilliant @attychang.bsky.social—landed the cover of the April issue of JCB! 🤩

@zidlab.bsky.social @tomo.science @hamid13r.bsky.social

Marketing aside, that 20 micron AFIS range does look pretty appealing for imaging big lamellae!

Her grandma was in the merch shop before the game last week getting a jersey and telling everyone how excited she was for the home debut - so very sweet!

The Tortured Proteins Department Podcast · Stephanie Wankowicz · A deep dive into scientific discovery and the process of doing science, hosted by Stephanie Wankowicz and James Fraser.

Since @stephanieaw.bsky.social left the lab to start her group at Vanderbilt, we've been talking regularly on the ups and downs of academic science. We started recording...

The Tortured Proteins Department

open.spotify.com/show/10PHVou...

(science with a small dose of running and Taylor Swift)

Dual axis stage vs some sharpie marks, who comes out ahead?

Thanks! Whoever manages to recruit Atty (ya-ting) as a postdoc is going to be living it up - she led sample prep, data collection, processing, and all of the new morphometrics programming.

I want one

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

Ope also with @zidlab.bsky.social - hard to keep up with who is on blue sky!

Subtomogram Averaging of a mitochondrially co-translating ribosome

Happy to share that the final version of record for our (
@nanigrotjahn.bsky.social) #teamtomo mitochondrial cotranslation story is online at @jcb.org! We combined STA with surface morphometrics to learn how ribosomes bind to and alter mitochondrial membranes in yeast.

rupress.org/jcb/article/...

Makes sense - fwiw, the trained dragonfly networks supposedly can be exported and run via python - but I haven't done it.

I use Alex rigort's cylinder tracing tools in Amira to convert the segmentation to picks. With a presegmented map it goes very fast - no false positives at all. Matt Swulius described that in his dragonfly Jove article, not my original idea...

For filaments, amira style segmentation (or dragonfly!) and then automated particle extraction is what has worked best for me!

I'm fond of tomotwin, but we still rely heavily on classical template matching.

Structure of the Thin Filament in Human iPSC-derived Cardiomyocytes and its Response to Heart Disease Cardiovascular diseases are a leading cause of death worldwide, but our understanding of the underlying mechanisms is limited, in part because of the complexity of the cellular machinery that controls...

www.biorxiv.org/content/10.1... #teamtomo #cryoET

Beautiful structures!