Mark Frank

Morris Bridge on a sunny Fall day.

Meanwhile in “war ravaged Portland.” #PDX

In situ structure determination of conformationally flexible targets using nextPYP - Nature Protocols The procedure for nextPYP facilitates the end-to-end processing of cryoelectron tomography data for high-resolution structure determination and conformational variability analysis.

Woo! My lab's Nature Protocols paper is out today.

In a nutshell, the protocol shows how to use our Cryo-ET software to solve high-res protein structures.

I don't think any of the other authors are here, but congrats to Hsuan-Fu, Ye, and Wendy for all of their work!

www.nature.com/articles/s41...

Structural dynamics of mitochondrial ATP synthase in Chlamydomonas reinhardtii revealed by in situ CryoET https://www.biorxiv.org/content/10.1101/2025.09.10.674987v1

I realize I don't post much, but figured I would share an update. As of today, I am officially supported by the Interdisciplinary Training in Microbial Pathogenesis and Immunology T32 Training grant.

Interior view of a hallway at OHSU with an inspirational quote on the wall reading "Is there a higher calling than curing cancer?" and the OHSU logo displayed.

"We couldn’t be more excited about the transformational potential of this work for humanity."

- Phil and Penny Knight on their historic $2 billion gift to @ohsuknight.bsky.social to transform the future of cancer care and set a new standard globally.

#GiveCancerHell

Took this photo of the Tilikum Bridge on my walk this morning. Beautiful weather this morning. #PDX

Gokul Adethya, Bhanu Pratyush Mantha, Tianyang Wang, Xingjian Li, Min Xu: SaSi: A Self-augmented and Self-interpreted Deep Learning Approach for Few-shot Cryo-ET Particle Detection https://arxiv.org/abs/2505.19948 https://arxiv.org/pdf/2505.19948 https://arxiv.org/html/2505.19948

This is really nice CryoET work and video.

paper link: www.science.org/doi/10.1126/...

‘Forever’ molecules arrange themselves into cell-like structures At sufficiently high concentrations, some of the compounds called per- and poly-fluoroalkyl substances self-organize into two-layered membranes.

‘Forever chemicals’ self-assemble into stable structures resembling biological cells — a behaviour that could help to explain why they stick around for decades in the soil or groundwater

https://go.nature.com/3F02sEd

This would have been so useful when I was first learning tomographic data processing back in 2019! Thanks for sharing!

I talked to @kakape.bsky.social about this for @science.org, along with many other colleagues including those with different views on regulatory oversight. We all agree: it’s too vague to be implemented, effective, or enforceable.

www.science.org/content/arti...

When the White House fact sheet says manipulates "viruses and other biological agents," it reads as potentially restricting a lot more than research on viruses of pandemic potential. I am concerned in terms of how this will ultimately be interpreted into policy.

“The Website” is here! It can be intimidating getting into analysis of #CryoET data, and software is evolving all the time👩‍💻🚀. @phaips.vd.st & @florentwaltz.bsky.social put our lab’s workflows into an online guide. We hope this helps lower the bar to joining #TeamTomo. Feedback much appreciated! 🧪🧶🧬🔬

Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!

tomoguide.github.io

Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪

Our latest paper is out! Congratulations to @leaswistak.bsky.social et al for this amazing #cryoET work that elucidates the initial stages of #T3SS dependent vacuolar damage during #Shigella infection. We will do a deep-dive later! journals.plos.org/plosbiology/...

🚨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

Figure 4. MemBrain v2 end-to-end workflow detects periodic phycobilisome organization. A: Raw tomogram slice of EMD-31244. B: Out-of-the-box MemBrain-seg segmentation (light blue). C: A single membrane instance can be visualized in Surforama and manually annotated with GT phycobilisome positions (magenta). D: MemBrain-pick localizes particles (trained with data from C) on all membranes in the tomogram. E: MemBrain-stats computes Ripley’s O statistic using the positions from D with a bin size of 5nm. The distance between peaks (35 nm) was measured to estimate chain unit spacings.

We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples!

Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵

#CryoET #TeamTomo
www.biorxiv.org/content/10.1...

Webinars The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…

Join us April 8th for a software webinar with @alisterburt.bsky.social from @genentech.bsky.social sharing the latest on Warp.

Warp
Alister Burt, Ph.D., Computational Scientist, Genentech
Tuesday, April 8, 2025 - 12:00pm ET

Register here: buff.ly/mXUYR4A

#SBGrid #Webinars #StructuralBiology

You always know the inevitable is going to happen sooner or later and you think you’re prepared, but you never are. Today my best friend of 20 years crossed the rainbow bridge. I’ll always treasure the memories we shared together. Rest well, Coco. 2004-2025

Folks, I can’t stress this enough:

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Honored to be part of this amazing work, where synaptic vesicle fusion has been studied by a clever combination of optogenetic stimulation and cryoET.

I welcomed the opportunity to contribute with mesoscopic simulations involving dynamic membranes. Preprint: www.biorxiv.org/content/10.1...

Text: EMBO is on Bluesky. Butterfly icon with text: @embo.org

Hello everyone on Bluesky! 🧪

We are EMBO, the organization of more than 2,100 leading researchers that promotes excellence in #lifesciences in Europe and beyond.

Read more: www.embo.org/about-embo/m...

TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms TomoCPT is a generalizable transformer-based 3D particle-picking tool for cryo-tomographic data.

Pranav N. M. Shah et al.: TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms #CryoET #ParticlePicking #SubTomogramAveraging @UniofOxford@IEUniversity...#IUCr https://journals.iucr.org/paper?S2059798325000865

Hey #teamtomo, if you often find yourself using the excellent membrain-seg from @lorenzlamm.bsky.social et al., you might find my napari plugin "napari-segselect" useful. Let's say your tomogram contains the edges of two bacterial cells, each with a membrane and cell wall:

My proposal for the Pacific Northwest Center for Cryo-EM has been approved! #CryoET #Victory

The Senate Finance Committee is about to vote on RFK Jr’s nomination. I tuned in late & missed the chair’s opening statements but now listening to Wyden talk about how unfit he is. The list is long.

New review on structural glycobiology in glycosciences: "From enzymes to organelles". Carbohydrate processing enzymes, glycosylation networks in vitro, Cryo-ET in direct visualisation of native biology , challenges for studying glycosylation by cryo-ET.
tinyurl.com/4jnv85xt

#glycotime

It's ironic how Wikipedia of all things, the bane of my secondary school teachers, remains the purest part of the internet these days.

I put together a small guide on how to get started with Fiji. Please distribute to anyone who might benefit form this! zenodo.org/records/1477... #imageanalysis #fiji #imagej #training

My first contributions to the grid graveyard. #Failure