Lukas Jarzembowski

Single-cell and isoform-specific translational profiling of the mouse brain - Nature Post-transcriptional regulation of mRNA translation was explored using Ribo-STAMP and single-cell RNA sequencing to reveal cell-type-specific and isoform-specific translation patterns across hipp...

Chuffed to see our paper with @geneyeo.bsky.social finally published in @nature.com.
www.nature.com/articles/s41...
Very grateful to Fede, Susie, and Dave from my lab, and Sammi, Eric, and Pratibha from Gene's lab. What did we find? ⬇️ ⬇️ ⬇️

And save >80% on the cost by pooling 6 or more plasmids into a single sample using our free SAVEMONEY algorithm!

elifesciences.org/articles/88794

colab.research.google.com/github/Masaa...

Excited to share our new paper and lipid- and protein-directed photocatalytic labeling method (POCA) just out in @natchembio.nature.com. tinyurl.com/2kcxuvvv. Big congrats to first author Andrew Becker and the whole team for launching our lab into the wild world of singlet oxygen interactomics.

Check out our newest findings on how #lysosomes are generated from #endolysosomes. Great work from @samit2104.bsky.social ! @biozentrum.unibas.ch , @unibas.ch #cellbio #cell #organelles
Ca2+ and DRP1 drive endocytic lysosome reformation at tripartite contact sites www.biorxiv.org/content/10.6...

CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis CRISPR screens in iPSC-derived neurons reveal that the E3 ubiquitin ligase CRL5SOCS4 ubiquitinates tau, that CUL5 expression is correlated with resilience in human Alzheimer’s disease, and that electron transport chain dysfunction alters tau degradation by the proteasome.

Now online! CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis

🧪 We are excited to share this novel open access paper on Phasor Mixing Coefficient to analyze colocalization, developed by folks @i2janelia.bsky.social and @aicjanelia.bsky.social. This is also the first technical paper jointly published with our sister imaging center @malacridalab.bsky.social!

Ideal efficacy photoswitching for chromocontrol of TRPC4/5 channel functions in live tissues - Nature Chemical Biology Using chemical photoswitchable reagents to exert purely wavelength-dependent control over biological systems in deep tissue and in vivo requires a concentration-independent design paradigm. Here, such...

A new paper by @thornsesholdlab.bsky.social reports photoswitchable ligands with wavelength-dependent, and concentration-independent, control of TRPC4/5 channels in live tissues

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

We have been thinking a lot recently on how to share and interact with code when doing image analysis. This is one piece of the puzzle. Awesome work driven by Bruno S.

Always a delight to work with @henriqueslab.bsky.social 🫶
More to come soon 😄.

Compact Calm1 promoter enables AAV mediated neuron-targeted expression in human iPSC-derived brain organoids - Scientific Reports Scientific Reports - Compact Calm1 promoter enables AAV mediated neuron-targeted expression in human iPSC-derived brain organoids

New paper out 🔥!

Small promoter, big potential🧬 We show that the ultra-compact Calm1 promoter efficiently targets human neurons in brain organoids and is a promising alternative to hSyn for AAV gene delivery.

Huge thanks to everyone who contributed to this work!
🧠 📄: www.nature.com/articles/s41...

iGlu3Fast and iGlu3Slow, improved fluorescent reporters for detection of spontaneous glutamate activity in the brain The genetically-encoded fluorescent glutamate sensor, iGluSnFR3, characterised by a high dynamic range and rapid on-kinetics, is an attractive sensor for glutamate imaging in the central nervous syste...

The latest version of our collaboration with Katalin Torok and her lab is up. We report some new glutamate sensors. Great work from Sara Bertelli in Berlin and the whole team in London (Holly & Oanh particularly).

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



1/6

On the first day of the Christmas holidays, I got... a new preprint out! Challenging the reproducibility of our manual presynaptic actin nanostructure identification: www.biorxiv.org/content/10.6...
(data from Bingham et al. @jcb.org 2023 doi.org/10.1083/jcb....) with @flevet.bsky.social

Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n

The vault associates with membranes in situ The eukaryotic vault particle is a giant ribonucleoprotein complex that assembles into an iconic barrel-like cage. Its cellular function has remained elusive despite extensive characterization. Using ...

Vaults. They are cell biology's greatest puzzle! This preprint from Martin Beck's lab shows them docked on ER membranes with a ribosome inside. What on earth is going on there??

#CellBiology #WTFology

www.biorxiv.org/content/10.6...

It’s FINALLY out! 🎉🚀 We have been working on PhotoFiTT for a long time, and it’s now published, introducing a quantitative framework to measure phototoxicity and optimise live-cell microscopy experiments. So excited to finally share the last version! 🔬✨ #PhotoFiTT doi.org/10.1038/s414...

PD-L2 Regulates Natural Antibody and IL-10 Secretion by B-1 cells B-1 cells are innate-like lymphocytes that play a critical role in homeostasis by secreting natural antibodies, typically IgM, and immunosuppressive molecules such as IL-10. However, the regulation of...

This #Preprint reports that B6 (but not wild mice) have a truncated PDL2, missing an active intracellular signalling domain:
"Surprisingly, in C57BL/6J (B6) mice PD-L2 has only a 5-amino acid intracellular domain, and the same is true for several other laboratory mouse strains"
#Immunology

Expression of H1R, H2R and H3R tagged with p2A-mCherry-N1 or p2A2-mCherry-N1 in HELA cells. A) H1R_p2AmCherry-N1 B) H2R_p2AmCherry-N1 C) H3R_p2AmCherry-N1. D, E and F show the H1R, H2R and H3R with p2A2mCherry-N1 respectively.

A reminder to use the right P2A sequence to produce separate proteins - the images are from a GPCR-P2A-mCherry construct using a P2A variant without (upper row) and with (lower row) a preceding GSG linker.

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...