Gav Sturm

Nellie's image analysis capabilities are vast. I put a video of yeast mitochondria through Nellie and generated a 'live-cell MitoGraph' - a topological graph capturing mitochondrial network's fission and fusion events over time.

Nellie is out in Nature Methods! Analyzing live-cell bioimaging is really hard. Nellie not only makes this analysis accessible but also brings out the full beauty of your data. Give it a try! (Nellie tracking mitochondria in Blender below).

In regular microscopy we image 2D objects to 2D images. However, a 'remote refocus' (RR) can image 3D objects to 3D images!

-> Here's a tiny 3D object imaged by RR. The 3D image 'floats' in the remote space, and can be reimaged in different ways.
-> This is the foundation of some new technologies!

The end of an era. After 9.5 years the York lab departs Calico with an incredible roster of projects and publications:

andrewgyork.github.io

-> It's been an honor to be part of this team and I wish @mariaingaramo.bsky.social & @andrewgyork.bsky.social the best on their new journey! What a ride ;)

For those who aren't biologists: This is a biosafety cabinet. Every biomedical research lab in the country has one or more of these bio safety cabinets. They use air flow to protect cells from contamination by bacteria and fungal spores while you are working with them.

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

Microscopy Nodes is now up on bioRxiv! 🚀

This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).

High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬

www.biorxiv.org/content/10.1...

The transient nature of pearling makes it hard to detect - in normal cells you might need to sit and watch one spot for a long time and then, if you blink, you'll miss it

Mitochondria (and other cytoplasmic structures) in tissue cultures Click on the article title to read more.

absolutely! well ahead of its time and not well known enough: onlinelibrary.wiley.com/doi/10.1002/...

yes but with suppressed curvature and reduced frequency.

Mitochondria consist of networks of cylindrical tubes, right? Not necessarily! - in our new preprint, @gavsturm.bsky.social investigates how mitochondria transiently adopt a beads-on-a-string morphology

www.biorxiv.org/content/10.1...

We hope you will enjoy these preprints. I will just close with this holiday wish to everyone who celebrates mitochondria: Happy Mito to all, and to all, a Good Mito!

I’m ultra excited about our preprints on mitochondrial pearling. In two concurrent collaborative studies with @wallaceucsf.bsky.social, we investigated its consequences on mtDNA nucleoids (led by @jclandoni.bsky.social) & its biophysical causes (led by @gavsturm.bsky.social). Funders HFSP, ERC, SNSF

Thanks to my PhD advisor @wallaceucsf.bsky.social and all of our amazing collaborators, our biophysical model lays the groundwork for understanding pearling as a essential mitochondrial dynamic; integrating ionic flux, inter-organelle interactions, molecular motors, and bioenergetics. 10/10

Studying this specific event goes all the way back to 1915, and has been given many names since. Take a close look at Margaret Lewis's hand-drawn mitochondria. However, a comprehensive model has been missing... 9/10

The imaging data here includes over a 1000 videos of 4D light-sheet images. Crunching through this much image analysis was only possible thanks to @austin-lefebvre.bsky.social brand new automated organelle tracking platform, Nellie, 8/10
github.com/aelefebv/nel...

How did we image this rapid event sometimes occurring within a second of time? thanks to @kayleyhake.bsky.social @andrewgyork.bsky.social & @amsikking.bsky.social @Calico we got to observe this biology with the best microscope in the word (imo), SNOUTY 7/10

Other possible functions of pearling are emerging. We captured spontaneous pearling in diverse cell types including in important physiological events such neuronal action potentials, in T cell immune synapses, and in replicative senescence. There are so many exciting possibilities ahead! 6/10

What is the functional utility of pearling? The brilliant investigation of @jclandoni.bsky.social .social and @sulianamanley.bsky.social establish mitochondrial pearling as the first and only known mechanism for mitochondrial DNA disaggregation and regular distribution. 5/10
bsky.app/profile/jcla...

It's all physics. Using creative microscopic perturbations we establish that the 19th century Rayleigh-Plateau Pearling instability is the only model capable of explaining this event. This lead us to 3 physical forces; tension, pressure, and elasticity regulating pearling. Video by @Caleb_J_Rux 4/10

You may be thinking of fission machinery. DRP1? a GTPase-like protein? but alas not quite! osmotic shock, ionophores, chemical fixation, membrane permeabilization, micro-needle force, laser-stimulation all induce mitochondrial pearling! we needed a more fundamental explanation…physics! 3/10

Warning. Once you see it, you can’t unsee it. Fast spontaneous movements in which mitochondrial tubules transiently convert to thinly connected spheres (i.e. like a pearled necklace). So what is this strange event? 2/10

2x Preprint drop!!! Mitochondrial pearling has arrived!
“The Biophysical Mechanism of Mitochondrial Pearling”.
“Pearling Drives Mitochondrial DNA Nucleoid Distribution” 1/10
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...

5/ and in neurons of the fly brain.

Delighted to share our new preprint on the cell biology and genome of Stentor pyriformis, a giant ciliate that maintains Chlorella endosymbionts in surface-associated microtubule baskets.

www.biorxiv.org/content/10.1...

Think mitochondria are networks of cylindrical tubes? not always! Check out poster by @gavsturm.bsky.social "Mitochondrial Pearling: an emerging class of organelle dynamics explained by a biophysical pearling instability" tomorrow Sunday Dec 15 11:45-12:45 B145

I know slow sadness. I've known loud sadness. Sadness like a blanket wrapped around your shoulders, your heart.

I was not expecting this panic. This otherworldly sense of wrongness. The urgent feeling that this wasn't how it was supposed to go.

Bereavement.

GitHub - HohlbeinLab/OpenMicroscopy: Non-comprehensive list of projects and resources related to open microscopy. Non-comprehensive list of projects and resources related to open microscopy. - HohlbeinLab/OpenMicroscopy

Non-comprehensive list of projects, hardware, software, and people related to #OpenMicroscopy. List could do with some updates, so please share and suggest additions! github.com/HohlbeinLab/...

Continuing to go through my trove of cool videos... here is a classic from my work with Philipp Keller's team at @hhmijanelia.bsky.social
A developing fly embryo imaged with a SiMView #lightsheet microscope augmented with our Autopilot self-alignment system.

www.nature.com/articles/nbt...
🧪🔬🪰💻

Excited to share our latest findings, now published @NatureNeuro www.nature.com/articles/s41...

We found unmyelinated axons exhibit pearls-on-a-string morphology's due to their membrane mechanical properties.

Threads will follow!

GFAP expressing #astrocytes in orange, IBA1 positive microglia in blue. Images from unsectioned rat hemisphere. #lightsheet #microscopy at #Vanderbilt