Jacques Augenstreich

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods!
📦 Ultrack — robust, scalable nD cell tracking
🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration
Let’s dive in! 👇
www.nature.com/articles/s41...
www.nature.com/articles/s41...

#ZebrafishZunday: Simultaneous tracking of 100 zebrafish larvae using open-source software. Credit to FastTrack (www.fasttrack.sh). 🧪

Mapping of Mycobacterial Enzymes Involved in Triacylglycerol Accumulation as Intrabacterial Lipid Inclusions Using Activity-Based Multitarget Inhibitor Probes Lipids play a critical role in the physiology, life cycle, and pathogenicity of mycobacteria. They largely participate in host–pathogen interactions and fulfill important functions ranging from cell w...

It is my real pleasure to share our ASAP article published in ACS Infect Dis.
Another great collaboration with @pierresantucci.bsky.social @canaanlab.bsky.social
@lkremer1.bsky.social
@ibmm-balard.bsky.social
@map-proteomique.bsky.social
and more...
Enjoy 😊

pubs.acs.org/doi/10.1021/...

We have updated our database of funding opportunities for Early-Career Researchers (private foundations, federal, international)

We have 456 entries, for which we provide $ amount, deadline, eligibility criteria, etc.

Download this massive database here for free: research.jhu.edu/rdt/funding-...

Schematic representation of Rab GTPases acting as “eat me” signals for selective autophagy.

In this week's #mitophagy papers, Rab GTPases take the centre stage, with a systematic study their role in autophagy, showing that multiple "Rabs" selectively mediate the degradation of mitochondria and other cellular components.

Thanks to @biomednews.bsky.social

biomed.news/bims-tofagi/...

Cell membranes sustain phospholipid imbalance via cholesterol asymmetry This work challenges a major assumption in cell biology by showing that lipid bilayers can have drastically different phospholipid abundances between their two leaflets. This lipid abundance asymmetry...

Groundbreaking study in Cell from @leventallab.bsky.social: phospholipid asymmetry is a defining feature of the plasma membrane and cholesterol fills the holes — major implications for how this membrane works. A #lipidtime must-read! www.cell.com/cell/abstrac...

Pleased to highlight a new preprint from the lab. This is the work of my longtime collaborator in the lab Allison Fay, who wanated to create new tools for disocvery biology in mycobacteria, specifically a new sysem for protein localizaton and proximity proteomics.

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

Shout-out to @pierredupuy.bsky.social and colleagues!
Excited to share our latest study, where we uncovered a previously unknown bacterial defense system in M. #tuberculosis: effluxosomes — dynamic membrane clusters that coordinate resistance to multiple toxic metals.
shorturl.at/Ek0HD
#MicroSky

Any1 is a phospholipid scramblase involved in #endosome biogenesis, say Jieqiong Gao, Christian Ungermann and colleagues (Osnabrück University): rupress.org/jcb/article/...

#Membrane #lipid #Organelles #Biochemistry

Excited to share our last study. Huge congrats to Sarah Monard, Arnaud Métais, @gclugo.bsky.social, @chrisverollet.bsky.social and all colleagues!
We have found a mysterious cell type inside TB lung lesions that seems neuron-like but isn't quite a nerve cell.
Let's dive in👇

shorturl.at/x4Sb5

Fiji 2024 Year in Review: Milestones and Roadmap Introduction The Fiji team at LOCI is pleased to share significant progress on several major initiatives as we work towards raising the technological standards of Fiji. These include Fiji 2.16.0, feat...

Wow, this is big: "Fiji can now be launched in a Python-first mode, where first Python is started, then Fiji is started via the PyImageJ library. In this mode, Fiji is fully integrated with the active Python environment"
forum.image.sc/t/fiji-2024-...

Luminescent sensing of conformational integrin activation in living cells Villari et al. present the generation of a luminescent reporter for a β1 integrin activation sensor (β1IAS). A siRNA HTS on β1IAS KI endothelial cells revealed previously uncharacterized regulators of...

Luminescent sensing of conformational integrin activation in living cells
www.cell.com/cell-reports...

#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...

1. A thread about the value of doing "slow science": When I was in grad school I heard this (likely apocryphal) story about one of my favourite scientists: Barbara McClintock.

It’s incredibly hard to study lipids in biological membranes on the nanoscale. You need near-perfect information on both membrane ultrastructure and lipid density, which usually isn’t attainable. Lipid-CLEM brought to you by @mathilda95.bsky.social changes that.
www.biorxiv.org/content/10.1...

A picture showing the different modules available on MyScope, these include: Microscopy Concepts, Scanning Electron Microscopy, Transmission Electron Microscopy, Light & Fluorescence Microscopy, Cryo-Electron Microscopy, X-ray Diffraction, Energy Dispersive Spectroscopy, Atom Probe Tomography, Focused Ion Beam, Scanning Probe & Atomic Force Microscopy, Secondary Ion Mass Spectrometry, Research Data Management, Work Health and Safety

Are you planning your lectures/course content for this year? Check out MyScope – our free #microscopy training website with theory, quizzes and microscope simulators 🧪

Developed by our experts, open to the global community: www.myscope.training
#openlearning

Captain Haddock looking very frazzled, saying, “What a week, huh?” Tintin leans into the frame and says, “Captain, it’s Wednesday.” Snowy is very excited about the drink he has found.

Fantastic resource for bio icons: NIH Bioart Source

Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, #icons, and brushes is freely available within the public domain. bioart.niaid.nih.gov

The #biovoxxel figure tools provide a convenient way in saving SVG vector graphic from Fiji and create publication figures in Inkscape.
Thanks to Ved Sharma those SVGs can now also be opened in the browser and even in Adobe Illustrator, if you really have to use it (I won't blame you 😉)

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...

I was looking forward to this one! An open source software for fast reconstruction of 3D structured illumination microscopy (SIM) from Xi Peng's lab : www.cell.com/the-innovati...
Matlab-based, code here: github.com/Cao-ruijie/F...

World’s first fully 3D-printed microscope made in under 3 hours The microscope cost less than £50 to build using an open-source design and a common 3D printer

Our fully 3D-printed microscope is featured in @newscientist.bsky.social www.newscientist.com/article/2462...

Thank you !

😎 awesome story! A must-read for a cellular-microbiologist working on Mtb! Congrats 🍾

Thank you !
Your story on OSBP came at the right time to help moving forward !

More in the article about the membrane repair, and who is probably repairing it when lysoview reappears and LC3 disappears.
I deeply thank everyone that got involved in this, in particular Volker that let me explore the crazy ideas I had sometimes.

The autophagosome itself was not getting acidic while showing some presence of LAMP1 so it did fuse with some acidic compartment without showing it with Lysoview.

When Lysoview (same stuff than Lysotracker) was added, it's more interesting where actually the acidity of the MCV is lost before LC3 recruitment, showing membrane damages. As seen below, the acidity could recover with a loss of signal of LC3, showing the membrane was intact again /repaired:

An intriguing observation was that LC3 recruitment on the Mtb phagosome (MCV) could be transient / reversible:

Dynamic interplay of autophagy and membrane repair during Mycobacterium tuberculosis Infection Author summary Autophagy is a cellular process that allows cells to digest internal materials and may help in the defense against pathogenic bacteria, including Mycobacterium tuberculosis (Mtb), the c...

The final version of our story on autophagy and time-lapse imaging is out: doi.org/10.1371/jour...
(Corrected one expected on the 14th). This questioned a bit the direct role of xenophagy to digest Mtb, but show that is appearance may be useful to track phagosomal integrity in time-lapse imaging 👇