Lukas Jarzembowski

Neuronal fatty acid oxidation fuels memory after intensive learning in Drosophila - Nature Metabolism Neurons are shown to use fatty acid β-oxidation as a fuel source for memory formation upon intensive learning in Drosophila, challenging the view that neurons are unable to use fatty acids for energy ...

Textbooks said neurons don’t burn fatty acids for energy🤔. Our study delivers the first in vivo demonstration that fatty acid oxidation in defined memory neurons fuels memory formation.

Closing chapter of my PhD 🥳, out today in Nature Metabolism💥 @natmetabolism.nature.com

De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy De novo protein design has emerged as a powerful strategy with the promise to create new tools. The practical performance of designed fluorophore binders, however, has remained far from meeting fluore...

Preprint drop! 🚨 Rhobin-tag your proteins and watch Saci glow at high temps! 🔥 Bright, photostable, live-cell imaging made possible with JF dyes. Huge thanks to @samjlord.bsky.social @acharlesorszag.bsky.social @mullinslab.bsky.social and Bo Huang lab at UCSF.😊

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

Daily ultrastructural remodeling of clock neurons A cluster of Drosophila clock neurons remodel their axonal arbors daily. Using volumetric electron microscopy at different times of day, Ispizua, Rodriguez-Caron, and colleagues reveal ultrastructural...

SO HAPPY to share our new paper in @currentbiology.bsky.social! Using volumetric EM, we found daily shifts in synapses, vesicles, and mitochondria that accompany neuronal remodeling, linking structural plasticity to changes in how s-LNv neurons influence their targets
www.cell.com/current-biol...

An enzymatic cascade enables sensitive and specific proximity labeling proteomics in challenging biological systems - Nature Communications Proximity labeling allows proteomic mapping of subcellular structures. Here, Sroka et al. develop in situ APEX activation (iAPEX) to overcome limitations of labeling specificity and H2O2 toxicity, app...

Thrilled to share "in situ APEX activation" (iAPEX), a proximity labeling technology for subcellular #proteomics applied to primary #cilia. iAPEX uses an enzymatic cascade, in which a D-amino acid oxidase locally produces H2O2 to activate ascorbate peroxidase.
www.nature.com/articles/s41...

Ever wondered if analyzing your images by using intensity Z-projections impacts your data?

Happy to announce my guest article in Microscopy & Analysis on that topic. It's a very short read but worth for everyone dealing with image analysis!

buff.ly/KJ147tI

#Microscopy #ZProjection #ImageAnalysis

ALFA nanobody-guided endogenous labeling - Nature Chemical Biology Small peptide tags (like ALFA) cause minimal disruption of proteins, but they typically lack fluorescence, which would enable knockin screening. Now, antigen-stabilizing fluorescent protein-fused nano...

Have you heard of #ANGEL?
Not this 😇, but ALFA Nanobody-Guided Endogenous Labeling #ANGEL - the new approach published by Wang et al. in @natchembio.nature.com Build on our ALFA® System, it enables direct fluorescent readout of #CRISPR knock-ins.

📄Full paper here: bit.ly/47XgK48

The Python Software Foundation was recommended for a $1.5M grant from the National Science Foundation. The terms of the award said PSF could not work on DEI, whether or not the grant funding was used for it.

PSF therefore declined the funding.

Science suffers, but commitment to core values remains

StayRose: a photostable StayGold derivative red-shifted by genetic code expansion Photobleaching of fluorescent proteins often limits the acquisition of high-quality images in microscopy. StayGold, a novel dimeric green fluorescent protein recently monomerised through sequence engi...

mStayRose is published in JBC 🥳🎉

Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable:

www.jbc.org/article/S002...

🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution.
www.biorxiv.org/cgi/content/...

Lipid Landscape of human cells Eukaryotic cells synthesise thousands of lipid species, yet the principles that organise them across compartments remain unclear. Here we introduce PAP-SL, parallel (immuno)affinity purification coupl...

#lipidtime alert!
This preprint by Kenji Maeda (cannot find him here) & colleagues is mandatory reading by everybody with even a cursory interest in lipid biology:
www.biorxiv.org/content/10.1...

mitochondria from bipolar patients are closer to the nucleus in these images; control patients' are spread out further

15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵

This is a beautiful piece of work - makes so many new approaches possible. Congrats to everybody involved!

Very exciting work. Shows how interfering with the levels of one lipid class leads to changes of other lipids that are not directly metabolically connected as the cell tries to maintain both lipid flux balance and biophysical membrane properties.

I’m happy to share some plugins I’ve been developping this summer: "Channels and Contrast" and LUTs Manager!
I can’t find new bugs and ideas by now so I need your help to please test them in your machines and report bugs, feedbacks and ideas! forum.image.sc/t/looking-fo...

⚠️ Half of commercial antibodies miss their target!
So how do you pick the right one for your experiment?

Here’s the solution 👉
Antibody characterization data (all tested in KO cells) are now available at:
🔗 onlygoodantibodies.co.uk

Tested by @ycharos.bsky.social & @oga-community.bsky.social

Everyone who does quantitative microscopy should read this! It’s amazing how many ways we can bias our imaging experiments without realizing we’re doing it.

Announcing our new PA biosensor, PILS-Nir1 – seen here in HeLa cells during PLC activation #lipidtime #phospholipids

Read the OA paper in JCB

Excited to share our preprint, now available online on BioRxiv! biorxiv.org/content/10.1.... We uncovered the coupling of translation and secretion machineries at the #axonalER to promote local delivery of axonal transmembrane proteins (TMPs) to the plasma membrane.

Previous preprint is now published in RSC Chemical Biology.
If you are interested in plasma membrane labeling, see the paper! 👇
pubs.rsc.org/en/content/a...

Bipartite Genetically Encoded Biosensors to Sense Calcium Ion Dynamics at Membrane–Membrane Contact Sites Self-complementing bipartite fluorescent proteins (FPs) are useful tools for the detection of protein–protein proximity and for localizing fluorophores to membrane–membrane contact sites. Here, we rep...

Bipartite Genetically Encoded Biosensors to Sense Calcium Ion Dynamics at Membrane–Membrane Contact Sites
pubs.acs.org/doi/full/10....

Genetic suppression features ABHD18 as a Barth syndrome therapeutic target - Nature The enzyme ABHD18 is shown to have a key role in cardiolipin metabolism in mitochondria, offering a potential route for a small-molecule treatment of the rare genetic disease Barth syndrome.

Nature research paper: Genetic suppression features ABHD18 as a Barth syndrome therapeutic target

go.nature.com/4n7dqbw

Our new collection offers cell biologists practical, expert-driven guidance and best practices in the design, execution, and analysis of experiments, and the subsequent communication of their results to their peers. 👉 rupress.org/jcb/collecti...

#Reproducibility

GitHub - DanuserLab/u-probe: Processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation... Processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation of th...

u-Probe now can be run without a MATLAB license, and exports detection and tracking results in a format that can immediately be visualized with @napari.org!
github.com/DanuserLab/u...

Check out this masterpiece of systematic #BioImageAnalysis 🤩

Don't fall into the trap.

Here are 5 corrections to keep in mind when interpreting RNAseq data:

(a thread)

DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations - Nature Methods DeepMVP is a deep learning framework for predicting PTM sites and variant-induced alterations across six modification types, including phosphorylation, acetylation, methylation, sumoylation, ubiquitin...

DeepMVP is a deep learning framework to predict PTM sites and variant-induced alterations across 6 common PTMs.

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

W… T… F…

Will anyone review this paper? Screening, sorting, and the feedback cycles that imperil peer review Scholarly publishing relies on peer review to identify the best science. Yet finding willing and qualified reviewers to evaluate manuscripts has become an increasingly challenging task, possibly even ...

1. Kevin Gross and I just posted a new science-of-science preprint.

This one explores the looming peer review crisis. As many of you know, it's becoming significantly more difficult for journal editors to find scholars willing to serve as peer reviewers for submitted manuscripts.

Out today in @nature.com: Together with the Honigmann, Shevchenko, Drobot and Hof labs, we present a general workflow for imaging the localization and transport of individual lipids in cells and mapping their metabolism.
www.nature.com/articles/s41...

There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...